use strict;
use warnings;
use Getopt::Long qw(GetOptions);
use IO::Uncompress::Gunzip qw(gunzip $GunzipError);

#Unzip .gz files into .txt files
# In command line run
# perl getOptsLong -orig <file1_name> -new <file2_name> 

my $input_1 = '';
my $input_2 = '';

GetOptions(
    'orig=s'=> \$input_1,
    'new=s' => \$input_2
           ) or die("Error in command line arguments\n");
unless ($input_1) {die "need to specify -orig";} 
unless ($input_2) {die "need to specify -new";} 
unless (-f $input_1) {die "no file '$input_1'";} 
unless (-f $input_2) {die "no file '$input_2'";} 

my $base_1 = $input_1;
$base_1=~s/\.gz$//i; 

my $base_2 = $input_2;
$base_2=~s/\.gz$//i; 

my $output_1=$base_1.'.txt'; 
gunzip $input_1 => $output_1       
    or die"gunzip failed:$GunzipError\n";

my $output_2=$base_2.'.txt'; 
gunzip $input_2 => $output_2
    or die "gunzip failed:$GunzipError\n";

my $csv_1=$base_1.'.csv'; 

#Convert to cvs 
open my $infile_1, "<", $output_1 or die $!;
open my $outfile_1, ">", $csv_1 or die $!;
#$header_1 = "Clock,Sinks,Buffers,Cells,Slew,Path,Vio,Area";
my $lines_1;
while(<$infile_1>){
    if(/(\w+|\S+)\s+(\d+)\s+(\d+)\s+(\d+)\s+(\d+.\d+)\s+(\d+.\d+)\s+(\
+d+)\s+(\d+.\d+)/g){
    tr/ /,/s;
    
    print $outfile_1 "$_";
    $lines_1 = $_;
    }else{
    #$lines_1 = $_;
    #warn "WARN: This line does not follow the normal output pattern, 
+";
    }
}

#print $outfile_1 $header_1;
print $outfile_1 "$lines_1\n";

close $output_1;
close $outfile_1;
unlink $output_1 or die "cant unlink $output_1 $!"; 

my $csv_2=$base_2.'.csv'; 

open my $infile_2, "<", $output_2 or die $!;
open my $outfile_2, ">", $csv_2 or die $!;

my $lines_2;
#my @columns_2 = ('Clock','Time','Waveform','Types','Sources');
while(<$infile_2>){
    if(/(\w+)\s+(\d+.\d+)\s+(.\d+\s+\d+.\d+.)\s+/g){

    tr/ /,/s;
    print $outfile_2 "$_";
    $lines_2 = $_;
    }else{
    #$lines_2 .= $_;
    #warn "WARN: This line does not follow the normal output pattern, 
+";
    }
}
#print $outfile_2 "@columns_2\n";
print $outfile_2 "$lines_2\n";

close $output_2;
close $outfile_2;
unlink $output_2 or die "cant unlink $output_2 $!";
[download]

To use Getopt::Long the receiving variables need to be defined first, notice the my's before the call

When using Getopt::Long you do not pass the value but a pointer to the storage location, that is what \$input_1 rather than $input_1 passes

Notice simple error checking for command line options

Notice how i determine a base name by removing the .gz from the end. if no .gz is at the end the original input name is used. Notice how i then add a .txt and .csv to that name to get the output file names

How to sort of hide them?
i just deleted(unlinked) them when they were no longer needed