use warnings;
use strict;
use Data::Dumper qw(Dumper);

my @clk =  ('ux_prim_clk', 'ux_side_clk', 'ux_xtal_frm_refclk');

#my @clk_output = map [ split /_/, $_ ], @clk;

# Just as a note: Performance is the same with explict loop.
# Every map statement can be expressed as a foreach() loop.
# This is the same your previous statement - nothing wrong with it
# just demo'ing what the map actually does...

my @clk_output; 
foreach my $clk_line (@clk)
{
   push @clk_output, [split "_",$clk_line];
}

print Dumper \@clk_output;

my @clk_new;
foreach my $row_ref (@clk_output)
{
    push @clk_new, join ("_",@$row_ref);
}

print Dumper \@clk_new;

__END__
$VAR1 = [
          [
            'ux',
            'prim',
            'clk'
          ],
          [
            'ux',
            'side',
            'clk'
          ],
          [
            'ux',
            'xtal',
            'frm',
            'refclk'
          ]
        ];
$VAR1 = 'ux_prim_clk';
$VAR2 = 'ux_side_clk';
$VAR3 = 'ux_xtal_frm_refclk';

##</code><code>##

use warnings;
use strict;
use Data::Dumper qw(Dumper);

my @clk =  ('ux_prim_clk', 'ux_side_clk', 'ux_xtal_frm_refclk');

my @clk_output = map [ split /_/, $_ ], @clk;

print Dumper \@clk_output;

my @clk_new = map{my $line =join ("_", @$_); $line}@clk_output;

print Dumper \@clk_new;