Why do I keep getting pop-up windows in Safari

Click here and follow the instructions, or if there’s a type of adware not covered by them on the computer, these ones. If you're willing to use a tool to remove it(you don't need to, but may find it easier), you can instead run Adware Medic; this link is a direct download.

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That option blocks popups opened automatically with JavaScript or other scripting, not those produced by adware.

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You shouldn't need to use malware/ad blockers. I tried all different things and nothing worked for Yosemite safari.

I did the following and it worked:

Safari - preferences - security - Internet plug-ins - click "website settings" - go through each point. Mine was embedded in Adobe Flash player. It was called "smart-search" so I blocked it and deleted it and this solved the issue.