The oft-misused word "which" is the basic problem in this passage. The rule of "which" vs "that" is simple, per Strunk & White's "The Elements of Style." As a general principle, the word "which" should be used only in a dependent clause. The word "that" should be used everywhere else. So in this passage, change the word "which" to "that" and it immediately fixes the lack of clarity. For example: "After introducing some anchors by the user, the range of nodes THAT are affected by a single anchor or a group of anchors should be specified." The phrase "the range of nodes that are affected" is an independent clause (makes a direct statement), even though it appears within a larger prepositional phrase/dependent clause (all prepositional phrases are dependent clauses) as introduced by the word "After..." Yes this sounds mighty confusing, but the trick is to look at the individual, smaller phrases that ultimately compose a larger, complex sentence.
The memory trick for this rule is called "The Comma Witch." If the word "which" appears it only should be in a dependent clause and therefore should be preceded by a comma, which is the punctuation mark that primarily defines a dependent clause. No comma before the "which" generally means that the phrase is an independent clause (also called a direct clause) and the word "which" should be changed to "that."
[CLARITY NOTE FOR ENGLISH LEARNERS: Because memory tricks (mnemonics) often rely on cultural or idiomatic concepts, I am adding here a literal explanation of the Comma Witch for those who are new to the English language and might not understand why this simplifies the way to remember a grammar rule. The word "witch" is a sound-alike pun for the word "which." Because the image of a witch is easy to remember, an individual then can use imagination to visualize a Comma Witch. It might be a witch riding on a comma-shaped broom, or wearing a comma-shaped hat, or with a comma appearing as a nose or as a facial wart... the possibilities are endless and the point is to invent something that works for you in your own mind. The ultimate goal is that picturing this "Comma Witch" permanently links the word "which" to a comma/dependent clause and reminds an editor to check for proper punctuation and word usage. END OF CLARITY NOTE FOR ENGLISH LEARNERS].
Regarding the answer to this question, the only way to properly use "which" in the provided sentence only makes it sound confusing/awkward: "After introducing some anchors by the user, the range of nodes, WHICH are affected by a single anchor or group of anchors, should be specified." Applying the "comma which" rule simplifies this statement (changes "which" to "that"), so that it a) clearly and concisely states its purpose, and b) is MUCH easier to read and understand.