I'd eval a dispatch table of operator functions into existence:

#! perl -slw
use strict;

my %ops;
for my $op ( qw[ < <= == >= > != lt le eq ge gt ne ] ) {
    $ops{ $op } = eval "sub{ \$_[0] $op \$_[1] }";
}

printf "Enter criteria: ";
my( $f, $op, $c ) = split ' ', <STDIN>;

local $\;
while( <> ) {
    my @f = split ',';
    print if $ops{ $op }->( $f[ $f ], $c );
}
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The advantages over using eval in the loop are:

1. Only those operators you choose are executed, thus avoiding the possibility of a user supplying an "operator" like system( ... ).
2. You only eval once for each operator; not for every line of the file.