APT is an excellent package manager. I don't remember ever having trouble with it. I do remember the dependency woes of earlier distros, but now it is generally as easy [if not easier] for me to install software on Linux as it is on Windows.
As for the topic [what were we talking about again? Oh yeah...] If nihil's suggestion does not work, I would second Wazz in suggesting Malware Bytes AntiMalware. I recently heard about another antimalware solution called RKill. I haven't had a chance to check it out, but I have heard pretty good things about it. Here is some info: