( while read command param; do  # whatever method
    files=`command param`       # to gather the files
    for file in $files; do      # process files
        echo $file
    done
done) | maincode.pl

##</code><code>##

#!/usr/bin/perl
use IPC::Open2;
my $cmd = 'whatever'; # really, I have no idea what you are doing
$pid = open2(\*CHLD_OUT, \*CHLD_IN, $cmd) or die "oops: $!\n";

while(<STDIN>) {
    chomp;
    my $file = $_; # now do whatever with $file.
    open(I,'<', $file);
    while (my $line = <I>) {
        ... # do whatever with each line in the file
    }
}