Usually it's a big single file of spaghetti, which is the bigger issue... I tend to try to separate logic branches (if/else) into separate functions. In addition to this, often a big if, with no else that just returns, I'll reverse the logic.

In then end, just like eating an elephant... one bite at a time. Eventually you'll have everything broken enough into separate functions that you then understand the whole better and can cleanly rewrite the whole thing.