Crossword clues that say 'layer' usually want you to think of different senses of the word, and I treat it like a little riddle where context does all the heavy lifting.
Sometimes 'layer' is literal: a stratum or tier — so words like 'stratum', 'tier', 'coat', 'ply', or 'lamina' might fit depending on the enumeration. Other times it's the biological use: a 'layer' can be a hen, the bird that lays eggs, so 'hen' is a classic short fill. If the clue's surface suggests geology or clothing, I start testing rock-related synonyms or words for garment layers. If it talks about building or roofing, 'felt' or 'shingle' might be on the table.
I also pay attention to whether the clue reads like a definition or a cryptic surface. In cryptics, 'layer' is usually the straight definition part rather than a wordplay indicator, but it could also appear in a phrase meaning 'to lay' (put, set) which gives verbs like 'lay' -> 'set' or 'put'. Cross-check with crossing letters and the clue length to narrow it down; that usually settles the debate for me and makes the grid click into place.