Substantive editing (or line editing) ensures that your document is considered professional, coherent, and compelling by eliminating the following:

Misspellings (including the ones overlooked by spell-checking programs)
Grammatical errors
Stylistic problems, such as capitalization and punctuation issues
Typos
Problems of usage
Problems of parallelism
Discontinuities
Ambiguities
Triteness
Awkward phrasing
Problems with references
Wordiness
Poor transitions
Contradictions
Organization problems
Retrievability problems
Lack of directness
Lack of concreteness
Lack of emphasis

From the foregoing you might assume that a substantive editor merely attends to a longer list of problems than does a copyeditor. The actual difference, however, involves how each editor focuses on the editing task.

The substantive editor takes a global approach to text. For example, the substantive editor might ask how does a manuscript flow from Chapter 1 through Chapter 3? Is the sequence logical? Is a more detailed explanation of the topic of extraction conditions required, or should the explanation be less detailed? Is the material in Chapter 6 overly redundant? While considering such global issues, the substantive editor corrects grammatical errors and makes other copyediting changes.

The copyeditor, on the other hand, takes a much more focused approach to the text. Unconcerned with global issues, the copyeditor focuses on grammar, spelling, word choice, sentence structure, and similar matters. (See Copyediting samples for a more complete definition of copyediting.)

To analogize, the substantive editor is like the president of a company, whereas the copyeditor is like the local branch manager.

The copyeditor’s job is to “decide which kinks or knots in someone else’s writing seems likely to disrupt communication with the intended readers and then to revise those patches as unobtrusively as possible” (Amy Einsohn, The Copyeditor’s Handbook: A Guide for Book Publishing and Corporate Communications). As a substantive editor, I satisfy these job criteria and go beyond them: I handle wildly inconsistent style, deal with factual errors, fix disorganized structure, identify fuzzy conclusions and incomplete references and then request clarification--all while observing the Hippocratic Oath, “First, do no harm.” I continually recognize that what I am editing is not my book; my job is to preserve the author’s voice while making the work readable, accurate, and consistent with whatever style is appropriate.

Much of the problem of unclear writing has to do with what cognitive scientist, linguist, and excellent writer Steven Pinker calls the curse of knowledge, “the difficulty in imagining what it is like for someone else not to know something that you know.” He explains further:

The curse of knowledge is the single best explanation I know of why good people write bad prose. It simply doesn’t occur to the writer that her readers don’t know what she knows—that they haven’t mastered the patois of her guild, can’t divine the missing steps that seem too obvious to mention, have no way to visualize a scene that to her is as clear as day. And so she doesn’t bother to explain the jargon, or spell out the logic, or supply the necessary detail.… To escape the curse of knowledge, we have to go beyond our own powers of divination. We have to close the loop, as the engineers say, and get a feedback signal from the world of readers—that is, show a draft to some people who are similar to our intended audience and find out whether they can follow it. This sounds banal but is in fact profound. Social psychologists have found that we are overconfident, sometimes to the point of delusion, about our ability to infer what other people think, even the people who are closest to us. Only when we ask those people do we discover that what’s obvious to us isn’t obvious to them. That’s why professional writers have editors.…

—The Sense of Style: The Thinking Person’s Guide to Writing in the 21st Century,
(New York: Viking, 2014), pp. 59, 61, 75.

That’s why you need an editor. (And that’s why I myself need an editor whenever I write.)

You can see a series of substantive editing samples, or you can examine any specific one from the following list of problems that substantive editing resolved.

Online samples

1. The interrogation (problems with point of view, coherence, and tense) Fiction
2. The interrogation continues (problems with coherence and static dialogue) Fiction
3. Book or books (problems with continuity and static dialogue) Fiction
4. The burly agent (problems with continuity, static dialogue, and mechanical style) Fiction (SPOILER)
5. Disliking students? (problem with character incongruity) Fiction
6. Drinks in hand (problems with logic and credibility as well as character incongruity) Fiction
7. The text message (problems with continuity—a serious plot hole— and static dialogue) Fiction (SPOILER)
8. The long first sip (problem with continuity—savoring a sip while talking and the pub’s location) Fiction
9. Setting the scene (problems with tense, emphasis, coherence, and mechanical style) Fiction
10. The hair flip (problems with muddied dialogue and garbled syntax) Fiction
11. To reschedule the interview (problems with continuity—establishing the day of the week—and pacing) Fiction
12. Smoke rising (problems with vagueness, lack of emphasis, and static, unmotivated dialogue) Fiction
13. Which direction? (problems with continuity—self-contradictory text—and word choice) Fiction
14. What next? (problems with coherent flow) Fiction
15. A sensitive conversation (problem with a setting incongruity) Fiction
16. Suicide on Wednesday night (problems with continuity—a serious plot hole) Fiction (SPOILER)
17. Digestive system emphasis and coherence (problems with emphasis, coherence, ambiguity, and tense) Fiction
18. Diagnosing mental health issues (problems with emphasis and coherence) Fiction
19. Disaster tourists (problems with lack of clarity: precision and logic) Fiction
20. Was he hitting on me? (problems with dialogue logic, incomplete repairs, and paragraphing) Fiction
21. Writing better than pulling weeds (problems with coherence and tense) Fiction
22. Quote-unquote for irony (problems with emphasis and precise contrast) Fiction
23. The debriefing (problems with emphasis, coherence, “talking heads” dialogue, and character incongruity) Fiction
24. A CNN interview (problems with syntax and paragraphing) Fiction
25. In the campus café (problems with point of view, syntax, paragraphing, and word choice) Fiction
26. The first date (problems with paragraphing, ambiguity, syntax, and word choice) Fiction
27. Lonely sometimes (problems with point of view and logic) Fiction
28. Incessant reminders (problems with continuity, mechanical style, and paragraphing) Fiction
29. The other sister (problems with vagueness and plot loose ends) Fiction
30. The landing time (problems with time incongruities, syntax, illogical or self-contradictory phrases, and word choice) Fiction
31. Before the wake (problems with continuity, scene setting, transitions, vagueness, and word choice) Fiction
32. Swiveling (problems with continuity and logic) Fiction
33. Fragile despair (problems with coherence, dialogue presentation, and character incongruities) Fiction
34. The dark pact (problems with emphasis, coherence, tense, and word choice) Fiction
35. The abbot’s command (problems with muffled speech and imprecise word choice) Fiction
36. The apprentice’s arrival (problems with coherence, continuity, awkward phrasing, and garbled syntax) Fiction
37. A wizard’s career (coherence issues, poorly constructed sentences, and awkward phrasing) Fiction
38. Before retiring to bed (problems with continuity, poor sentence construction, and word choice) Fiction
39. Someone interfered (revision to establish the scene’s appropriately sinister mood) Fiction
40. Elaine is not human (problems with dialogue, internal contradiction, and emphasis) Fiction
41. A patriotic teenager (problems with ambiguity and modifiers) Fiction
42. May and June 1970 (problems with time) Fiction
43. The computer interface (problems with connotation issues, “talking heads” dialogue, scene setting, and overall mood) Fiction
44. Welcome back! (problems with continuity, word choice, garbled syntax, weak verbs, and vagueness) Fiction
45. His genetic match (problems with emphasis and coherence, “talking heads” dialogue, and scene setting) Fiction
46. A new chapter (problem with overall organization of chapters, redundancy, incorrect statements of fact, and need for context) Memoir
47. Strong bond (redundancy and text out of coherent chronological order) Memoir
48. The royal client (problems with ambiguous syntax and statements of fact) Memoir
49. Former wife (problems with mechanical style and fact) Memoir
50. Placement of context (problems with context, coherence, redundancy, and mechanical style) Memoir
51. Visiting the World Trade Center (problems with mechanical style and lack of clarity) Memoir
52. The legal clinic opens (problems with scene setting, syntax, context, facts, and overall consistency) Memoir
53. Clauses added to the lease (problems with continuity, faulty syntax, jargon, and transitions) Memoir
54. My father (problems with narrative flow, point of view, and accuracy of citations) Memoir
55. Apocalypse themes (problems with scriptural citations, format and figure placement, word choice, and readability) Religious (Christian)
56. Light upon light (problems with scriptural citations, transliteration, and U.S. conventions) Religious (Muslim)
57. Shari‘a law in China (issues of transliteration of both Chinese and Arabic, historical accuracy, word choice, and citations) Academic (ethnography)
58. Dispute resolution in China (problems with inconsistent focus, extraneous verbiage, and flat “academese” language) Academic (ethnography and law)
59. Social insurance in India (problems with redundancies, lack of precision, and confusing syntax) Academic (economics)
60. Introduction to Your Story Told (problems with emphasis, coherence, structure, style, terminology, and accuracy of quotations) Creative-writing how-to
61. What do agents and casting directors look for? (poorly organized text) Popular how-to
62. OK for 1966? (anachronistic language and other problems) Screen play
63. Out of character (characterization problems) Screen play
64. A nondisclosure agreement (a light-handed edit of "legalese") Legal

Hard-copy samples

65. Boilerplate information (one strange word) Technical
66. Concerning the readers of this manual (lack of directness and other problems) Technical
67. Inserting the diskette (how many times?) Technical
68. Connecting the video interface cable (an apparent contradiction in the instructions) Technical
69. Handling a diskette (a nonnative writer's malaprops) Technical
70. What is a macro? (more malaprops) Technical
71. Checking for matches (lack of concreteness, wordiness, and other problems) Technical
72. Limitations with the refresh rate (ambiguity, awkward phrasing, and other problems) Technical
73. Making the content fit (blather) Technical
74. Serving your digital needs (wordiness and many other problems) Technical