Verified answer

Temp cleanup + quick scan and remove + system restore dump and recreate = full scan - 95% the time

By President and CEO of Malwarebytes'-RubbeR DuckY-Marcin Kleczynski

http://forums.malwarebytes.org/index.php?s=&showto...

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http://forums.malwarebytes.org/index.php?showtopic...

You could follow this guide as a reference

Basic Malware Removal Guide

http://vmsar.wordpress.com/basic-malware-removal-g...

2

MalwareBytes, like all other anti-malware products, remove viruses, adware, etc by creating lists of what is harmful and generating batch files to remove the malware before it can react.

So in answer to your question, it can remove it if it has been added to the definition lists for MalwareBytes. Run a full scan for best results.

if the popup ads are caused by an Adware or Spyware then MalwareBytes will stop them. but it dose not stop normal popup ads inside a website. for that purpose you may download a POP UP BLOCKER from google, its free and a litlle app