You can supplement your Malwarebytes Anti-Malware scan with some other tools Firefox users have found effective. See: Troubleshoot Firefox issues caused by malware.

But it also makes sense to check a couple of things manually.

(1) Extensions installed in Firefox

Open the Add-ons page using either:

• Ctrl+Shift+a
• orange Firefox button (or Tools menu) > Add-ons

In the left column, click Extensions. Then take a careful look and disable everything you either don't recognize or don't use regularly. If Firefox prompts you to restart to make the change effective, you can do that as the last step after completing your review of the list.

(2) Windows Control Panel, Uninstall a Program

Click the "Installed on" column heading to bring the most recent infections, I mean, additions, to the top. This is useful in revealing bundles that may have snuck unwanted software onto your PC. Remove everything you don't remember choosing intentionally.

Any improvement?

Maybe a stupid question ... but you say you have installed Malwarebytes, but did you also do the normal or extensive scan with it?
Plus, what kind of pop ups do you get? Only when using your browser or also when you are on your desktop when you say "new windows"?

Go to the Mozilla Add-ons Web Page (There’s a lot of good stuff here) and get a good add / pop-up blocker.