Как обработать разницу в функции MFCC для аудио файла

То же, что и @ zx81's (*SKIP)(*F), но с использованием отрицательного утверждения lookahead.

(?m)(?:if\(.*?\/\/endif|\([^()]*\))(*SKIP)(*F)|\b\d+\b(?!.*\.$)

DEMO

В python я бы сделал легко например,

import re
string = """cat 123 sat.
I like 000 not (456) though 111 is fine
222 if(  //endif if(cat==789 stuff  //endif   333"""
for line in string.split('\n'):                                  # Split the input according to the `\n` character and then iterate over the parts.
    if not line.endswith('.'):                                   # Don't consider the part which ends with a dot.
        for i in re.split(r'\([^()]*\)|if\(.*?//endif', line):   # Again split the part by brackets or if condition which endswith `//endif` and then iterate over the inner parts.
            for j in re.findall(r'\b\d+\b', i):                  # Then find all the numbers which are present inside the inner parts and then loop through the fetched numbers.
                print(j)                                         # Prints the number one ny one.

Выход:

000
111
222
333