require 'rubygems'
require 'ruport'

puts Ruport::Data::Table.load( ARGV.shift, :csv_options => { :col_sep 
+=> "\t" } ).sub_table( ARGV ).as( :csv )
[download]

Of course if you maybe showed what you've tried so far you might get some actual help with Perl code instead.

use v6;
my $data = q[colname1 colname2 colname3
  val1     val2        val3
  val11    val21      val31
  val12     val22       val32];

my @lines = $data.split: "\n";
my @rows;
my @header = @lines.shift.words;
for @lines -> $l {
    my %h = @header Z $l.words;
    @rows.push: {%h};
}
say @rows.perl;
my @colname = <colname1 colname3>;

say @colname.join("\t");
say $_{@colname}.join("\t") for @rows;
[download]

Though I admit that the output could be formatted a bit prettier, and some parts of the code are ugly hacks.

You may find Text::CSV_XS is helpful.

Code winds up with an ordered list of column positions to print and then does that for the data in the file by using list slice.

#!/usr/bin/perl -w
use strict;

my @desired_cols = qw(colname1 colname3); #order matters here

# reads first line to get actual column names

my $header_line = (<DATA>);
my @actual_cols = split(/\s+/,$header_line);

# get column number of the actual column names

my $pos =0;
my %col2_num = map {$_ => $pos++}@actual_cols;

# translate the desired col names into position numbers
                              
my @slice = map{$col2_num{$_}}@desired_cols;               

print join("\t",@desired_cols),"\n"; #header line
while (<DATA>)
{
   my @row = (split)[@slice];
   
   print join("\t",@row),"\n";       #each data row
}


=pod
Prints:
colname1    colname3
val1    val3
val11    val31
val12    val32
=cut

__DATA__
colname1 colname2 colname3
  val1     val2        val3
  val11    val21      val31
  val12     val22       val32
[download]

Two of Corion's code contributions may be of interest:

• join - join two files according to a common key
• part - split up files according to column value

This reads like the infamous make-my-homework request. You might have more success when also providing a short version of the Perl code you're currently using (that survives perl -c, which @colname={colname1,colname3} probably won't (excluding subs)).

Darn it, should have checked once more before pressing create; such a tempting opener, and I was too slow...

#!/usr/bin/perl

use strict;

my @required_cols = qw( colname1 colname3 colname4 );
my %record;

while (<DATA>) {
    my (@temp_data) = split( /\s+/ );
    push( @{ $record{$_} }, $temp_data[$_] )
      for (0 .. $#temp_data);
}

my (%final_data, $count);
for my $i ( keys %record ) {
    $count = 0;
    for my $j ( @{ $record{$i} } ) {
        push( @{ $final_data{$count} }, $j )
          if ( grep /\b$record{$i}->[0]\b/, @required_cols );
          $count++;
    }
}

print "@{ $final_data{$_} }\n" for ( sort keys %final_data );

__DATA__
colname1 colname2 colname3
val1 val2 val3
val11 val21 val31
val12 val22 val32
[download]