It really depends on the nature of the pages. If they contain any PHP code at all, that code needs to be moved to MODx snippets -- otherwise, the code will no longer execute in MODx.
In addition, you’ll want to pull out any HTML code and content that’s duplicated across pages and put it in either a MODx template or in one or more chunks.
It’s theoretically possible to do some of this with an editor that allows multi-file regular expression search and replace, but it might be faster to do it by hand than to figure out how to make that work.
You could also write PHP code (or Perl or something else) to transform the pages and remove the stuff that’s going in snippets, templates, or chunks, but -- again -- it might be faster to do it by hand, depending on your coding skills.
You might find some useful information here:
http://bobsguides.com/porting-your-site-to-modx.html
I’ve been there (though not with that many pages) and I generally use cut-and-paste. I can tell you that you’ll be very happy when you’re done -- it’s well worth the effort.