I'm having difficulty understanding exactly what you want. Perhaps you could include a brief sample of f1, f2 and the desired output.

A few things you need to cleanup while you are working on this:

• $line=split ... will only catch the # of elements resulting from the split. Be sure to have an array on the left-hand side, not a scalar
• Your second foreach is missing it's curly braces
• I'm not sure what you are trying with $_="CLAUSE_START=$line";, but I don't like seeing $_ on the left-hand side of an assignment
• This is probably just your pseudocode, but if not, when looping through files, be sure to open and close them within the loop and essentially loop through the elements in your array of filenames (i.e., foreach (@f1_filenames) )

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