Regardless, split(/\C/, $_) is still wrong. You want split(//, $_) instead. That will split "314" up into "3", "1", and "4" like you want.

Also, you don't need to declare them as global with our. Declare varaibles with my instead, when you first use them:

#!/usr/bin/perl -w
#filename: myMutator.pl

use strict;

my $file = shift || "myFiles/pi.txt";
open(FILE, "< $file") or die "Couldn't open $file: $!";

my @numberMutation;
while (<FILE>)
{
        chomp;
        push(@numberMutation, split(//, $_));
}


my @organism = (1,1,1,1,1,1,1,1,1);
foreach my $currentMutation (@numberMutation)
{
        my $i = 0;

        foreach my $currentGene (@organism)
        {
                if ($currentGene < $currentMutation)
                {
                        $organism[$i] = $currentMutation;
                        $i++;
                }
        }
}

foreach my $someGene (@organism)
{
        print "$someGene\n";
}

foreach my $thisMutate (@numberMutation)
{
        print "$thisMutate\n";
}
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I'm still not quite sure what you're trying to do, but if the file only contains a single line, you can avoid using a loop to read from it and just do this:

chomp(my $line = <FILE>);
my @numberMutation = split(//, $line);
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To follow up, here's some code indicating what split /\C/ does:

#!perl -w
use strict;
while (<DATA>) {
    chomp;
    warn "input line is '$_'\n";
    my @t = split /\C/, $_; 
    warn "split to [n=@{[ scalar @t ]}]: '@t'\n";
}

# input line is '31415926'
# split to [n=0]: ''
# input line is '12345678'
# split to [n=0]: ''

__DATA__
31415926
12345678
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