I would make 3 tables :
FILE (Contains ID and File Name, and possibly # of lines, or some indicator of size);
REGEX (Contains an ID, the Regex)
OCCURRANCE (Contains Regex_ID, FIle_ID, Line number).

You can pick a regex from the REGEX table, and find all occurrances from the OCCURRANCE table.

Obviously, run a batch process to populate the tables.

Consider SQLite, if you want a fast, very lightweight,free database.