Since you don't tell us what the output should be, I can only give you some general advice.

First, always do this:

use strict;
use warnings;
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And declare your variables with my. It helps t catch common errors.

Secondly, you can replace your two outer loops with something as simple as

while (<>) {
    # the current line is in $_, 
    # the current filename in $ARGV
}
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Thirdly if you want to group data by the ID, store that data in a a hash keyed by the ID.

And finally there's the unpack function for extracting fixed width data, and perlpacktut contains a nice tutorial-style introduction on how to use it.

And really-finally: If your data format has a name, go to CPAN and search for it - maybe there's already a module that does most of your work.