How do I remove flash pop-ups from Safari?

Question

Hi.
Up until now, Safari has been working perfectly. I constantly have flash pop-up ads opening in new windows (e.g. MacKeeper, MediaDownloader etc) or just flashing on Youtube, my email pages and in Google. It is driving me insane. I have researched on how to try and remove this. When I turn off my plug-ins, then they seem to disappear. However, I have always had my plug-ins turned on and have never had this problem before. I have tried to remove the plug-ins, but it won't let me. Is there anyway to fix this? Is it possible for me to remove Safari all together and then download it from the App Store?
PS: I have OSX 10.9.2
Please help.
Thanks,
Charel R

Answer 1

Helpful Links Regarding Malware Problems
If you are having an immediate problem with ads popping up see The Safe Mac » Adware Removal Guide and The Safe Mac » Adware Removal Tool. Open Safari, select Preferences from the Safari menu. Click on Extensions icon in the toolbar. Disable all Extensions. If this stops your problem, then re-enable them one by one until the problem returns. Now remove that extension as it is causing the problem.
An excellent link to read is Tom Reed's Mac Malware Guide.
Also, visit The XLab FAQs and read Detecting and avoiding malware and spyware.
See these Apple articles:
  Mac OS X Snow Leopard and malware detection
  OS X Lion- Protect your Mac from malware
  OS X Mountain Lion- Protect your Mac from malware
  OS X Mavericks- Protect your Mac from malware
  About file quarantine in OS X
If you require anti-virus protection Thomas Reed recommends using ClamXAV. (Thank you to Thomas Reed for this recommendation.)
From user Joe Bailey comes this equally useful advice:
The facts are:
1. There is no anti-malware software that can detect 100% of the malware out there.
2. There is no anti-malware that can detect anything targeting the Mac because there
     is no Mac malware in the wild, and therefore, no "signatures" to detect.
3. The very best way to prevent the most attacks is for you as the user to be aware that
     the most successful malware attacks rely on very sophisticated social engineering
     techniques preying on human avarice, ****, and fear.
4. Internet popups saying the FBI, NSA, Microsoft, your ISP has detected malware on
    your computer is intended to entice you to install their malware thinking it is a
    protection against malware.
5. Some of the anti-malware products on the market are worse than the malware
    from which they purport to protect you.
6. Be cautious where you go on the internet.
7. Only download anything from sites you know are safe.
8. Avoid links you receive in email, always be suspicious even if you get something
    you think is from a friend, but you were not expecting.
9. If there is any question in your mind, then assume it is malware.