while ( !eof FIRST ) {
    my $i = 0;
    my ( @first_lats, @first_lons );
    while ( !eof FIRST and $i < 10000 ) {
        $_ = <FIRST>;
        if ( $csv->parse( $_ )) {
            my ( $lat, lon ) = $csv->fields;
            $first_lats[$i] = $lat;
            $first_lons[$i] = $lon;
            $i++;
        } else {
            # report csv error
        }
    }
    check_distances( $i, \@first_lats, \@first_lons );
}

sub check_distances
{
    my ( $n, $flat, $flon ) = @_;

    open SECOND, "second.file" or die $!;
    while (<SECOND>) {
       if ($csv->parse($_)) {
           my ( $slat, $slon ) = $csv->fields;
           for ( my $i=0; $i<$n; $i++ ) {
               # check distance from $slat,$slon to $$flat[$i],$$flon[$i]
           }
       }
    }
}