Untested.

my %files

for my $file (@files) {
    my ($name,$sfx) = split'.', $file;
    open FILE, '<', $file or doe $!;
    push @{ $file{$name}{$sfx} }, <FILE>;
    close FILE;
}

for my $uniq ( keys %files ) {
    for my $sfx ( 'a' .. 'c' ) {
        for my $line ( @{ $files{$uniq}{$sfx} } ) {
            #do something with line
        }
    }
}
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