You could...

LINE:
 while(<IFH>) {
      chomp;
      my($nx,$ny) = split;

      next LINE if ($ny <= 1.0);

      CONDITION:
      foreach my $cond_ref ( @range_destination ) {
          my ( $min, $max, $dest ) = @$cond_ref;
          if ( $nx > $min && $nx < $max ) {
              $capVal_Hash{$dest}{$nx} = $ny;
              last CONDITION;
          }
      }
}
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One loop instead of two will save some time, I reckon.

If you know the frequency of values in your input, you can also order the @range_destination list so that the more frequent conditions are first, short circuiting the CONDITION loop faster.