If I understand your problem correctly, you want to break out of the loop after you find your number. Try adding last; to the end of your if block:

              if ($found[0] == $short_nums[$i])   {
                    push @new_array,  $nums[$i];
                    last;
              }
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Another problem you might be having is that it's very hard to check for equality with floating-point numbers with any consistency, because of strange rounding errors. If you always want to use 3 digits to the right of the decimal point, multiplying the numbers by 1000 and storing them as integers might give you better consistency. For example:

@short_nums = (99, 68, 86, 24);
...
              if (int($found[0]*1000) == $short_nums[$i])
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