This is my guess of how to implement my interpretation of your query:

use strict;

# get parameters from command line
my $fname1 = shift;
my $fname2 = shift;
my $fnameout = shift;

# read in all numbers from file 2 into a hash
open( FIN, "<$fname2" )
  or die( "Cannot open $fname2: $!" );

my %exclude_num = ();
while ( defined( my $line = <FIN> ) ) {
    # remove trailing newlines
    $line =~ s/[\r\n]+\z//s;

    # store number in hash
    $exclude_num{$line} = 1;
}

close( FIN );


# read in numbers from file 1, skipping excluded numbers
open( FIN, "<$fname1" )
  or die( "Cannot open $fname1: $!" );

open( FOUT, ">$fnameout" )
  or die( "Cannot create $fnameout: $!" );

while ( defined( my $line = <FIN> ) ) {
    # remove trailing newlines
    $line =~ s/[\r\n]+\z//s;

    # skip excluded numbers
    next if ( $exclude_num{$line} );

    print( FOUT "$line\n" );
}

close( FOUT );
close( FIN );
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