G'day LinuxMatt,

Here's the basis of how I might approach this:

$ perl -Mwarnings -Mstrict -E '
    my @test_data = (
        "comment follows: #qwerty",
        "  whitespace at start",
        "whitespace at end  ",
        "Total: some total",
        ", starts with a comma",
    );

    my @all_patterns = (q{#.*}, q{^\s+}, q{\s+$}, q{^Total}, q{^,});

    my @files = qw{file1 file2 file3};

    my %file_filters = (
        file1 => [0, 2, 4],
        file2 => [2, 1, 3],
        file3 => [4, 3, 2]
    );

    for my $file (@files) {
        say "File: $file  Patterns: @all_patterns[@{$file_filters{$fil
+e}}]";
        my @this_files_data = @test_data;
        for my $line (@this_files_data) {
            say "Start: |$line|";
            for (@{$file_filters{$file}}) {
                $line =~ s/$all_patterns[$_]//;
            }
            say "End:   |$line|";
        }
    }
'
File: file1  Patterns: #.* \s+$ ^,
Start: |comment follows: #qwerty|
End:   |comment follows:|
Start: |  whitespace at start|
End:   |  whitespace at start|
Start: |whitespace at end  |
End:   |whitespace at end|
Start: |Total: some total|
End:   |Total: some total|
Start: |, starts with a comma|
End:   | starts with a comma|
File: file2  Patterns: \s+$ ^\s+ ^Total
Start: |comment follows: #qwerty|
End:   |comment follows: #qwerty|
Start: |  whitespace at start|
End:   |whitespace at start|
Start: |whitespace at end  |
End:   |whitespace at end|
Start: |Total: some total|
End:   |: some total|
Start: |, starts with a comma|
End:   |, starts with a comma|
File: file3  Patterns: ^, ^Total \s+$
Start: |comment follows: #qwerty|
End:   |comment follows: #qwerty|
Start: |  whitespace at start|
End:   |  whitespace at start|
Start: |whitespace at end  |
End:   |whitespace at end|
Start: |Total: some total|
End:   |: some total|
Start: |, starts with a comma|
End:   | starts with a comma|
[download]

Be aware how the order of the patterns matters. At the start of the output, you'll see:

File: file1  Patterns: #.* \s+$ ^,
Start: |comment follows: #qwerty|
End:   |comment follows:|
[download]

However, had those first two patterns been reversed, you'd see:

File: file1  Patterns: \s+$ #.* ^,
Start: |comment follows: #qwerty|
End:   |comment follows: |
[download]

Note the extra space after "comment follows:".