Push your md5 sum onto the array in same order as your file array,
#!/usr/bin/perl -w
use strict;
@files = <*>;
foreach $file (@files) {
print $file . "\n";
}
foreach $file (@files) {
push(@md5,`md5sum $file`); #md5[n] has sum for file[n]
}
foreach $entry (@md5) {
print $entry . "\n";
}