I'd get rid of the malware first, because it's generally very annoying to have on your computer (I suppose you get all sorts of pop-up ads and/or your computer is slowed down). It's also possible it influences different settings, your Display settings for example. What is the malware you found? Have you tried running Malwarebytes to remove it?
You can get Malwarebytes here (it's free) : https://www.malwarebytes.com/antimalware/mac/
If Malwarebytes doesn't help, don't worry, you can still remove it, it just means you'll have to find the files to delete yourself. Tell us which malware you have and we'll help you.
As for the screen, I would try different screen resolutions. When you go in your System Preferences, in Display, you should be able to select a resolution. I recommend reading this article : http://www.imore.com/how-change-display-settings-your-mac
Just to make sure, are you only using the display that is part of the Macbook or are you using one or more external displays?