What you are really doing is selecting records from a database with the criteria provided in another file. Everytime you think "database", think "DBI" and use the power of CPAN to make life easier for you.

Look at the following:

use Modern::Perl;
use Data::Dump qw/dump/;
use SQL::Abstract;
use DBI;

my $dbh = DBI->connect(
    'dbi:CSV:',
    '', '',
    {
        f_dir        => './DB/',
        csv_sep_char => "\t",
    }
) or die "Cannot connect: $DBI::errstr";

my @where;
{
    my $query = 'SELECT * FROM filter_file ORDER BY orde';
    my $sth   = $dbh->prepare($query);
    $sth->execute();

    while ( my $row = $sth->fetchrow_hashref ) {
        push @where,
          { $row->{'column'} => { $row->{'relationship'} => $row->{'va
+lue'} } };
    }
    $sth->finish();
}
my $sql = SQL::Abstract->new;
my ( $where, @bind ) = $sql->where( \@where );

{
    my $query = "SELECT a, b, c FROM input $where";
    my $sth   = $dbh->prepare($query);
    $sth->execute(@bind);

    while ( my $row = $sth->fetchrow_hashref ) {
        say dump($row);
    }
    $sth->finish();
}
[download]

Output:

{ a => 0.2, b => "abc", c => 0.3 }
{ a => 0.1, b => "abd", c => 0.3 }
{ a => 0.4, b => "abe", c => 0.2 }
{ a => 0.1, b => "abc", c => 0.5 }
{ a => 0.1, b => "abd", c => 0.8 }
[download]

This script fetches the filter conditions from the filter_file, stuffs it into a SQL::Abstract data-structure, constructs an SQL query out of it that combines all filters at once (the "where" part of the SQL is  WHERE ( ( a <= ? OR c <= ? OR b = ? ) )) and then runs that SQL query against your input file.

No repeated going through your input file; clean and fast code; easy to understand, maintain and change for anyone who knows the basics of SQL.

A few caveats though:

• I had to change the name of your order column to orde since "order" is a reserved SQL keyword.
• As we are now dealing with SQL, the "equals" test is always =, even for strings so I had to change your eq in the filter_file to =.