Your problem description, example and code don't seem to be consistent so the following is a guess at what you may be after:

#!/usr/bin/perl
use warnings;
use strict;

my $str1 = <<STR;
col1    col2    col3
1    4    7
2    5    8
3    6    9
STR
my $str2 = <<STR;
col1    col2    col3
1    44    77
2    55    88
3    66    99
STR

for my $spec ([$str1, qw(col1 col3)], [$str2, qw(col3)]) {
    my ($file, @wantedCols) = @$spec;

    print "@wantedCols\n";

    open my $fIn, '<', \$file;
    
    my $index = 0;
    my %fileCols = map{$_ => $index++} split /\s+/, <$fIn>;
    my @slice = map{exists $fileCols{$_} ? $fileCols{$_} : ()} @wanted
+Cols;
    while (<$fIn>) {
        chomp;
        print join (' ', (split /\s+/)[@slice]), "\n";
    }
}
[download]

Prints:

col1 col3
1 7
2 8
3 9
col3
77
88
99
[download]

Note the "string as file" trick used to make the sample self contained and printing to stdout (for the same reason) will need to be changed to suit your real application of course. But using a self contained script like this as a test bed can speed up development and testing a lot because you don't need to juggle multiple files during testing.

Note too the three parameter open and the use of lexical file handles. Both things you should get into the habit of using.