You should also be aware, according to the Malware website product information, that the free version does not provide 'Real-Time Active Malware detection'.
In that case, you need to make sure that you have another Anti-virus protection package active that does provide real-time detection and prevention.
If you don't currently have one in place I suggest download and install of 'Microsoft Security Essentials' which is available free from:
True but Malware bytes isn't a substitute for an AV app anyway. Personally I prefer these scans to be non real time, slowing the PC. Just as long as the AV runs permanently.
If you've got the PRO version on your computer, you won't be able to install the free version. (Even uninstalling the PRO version first leaves something on your PC which stops the necessary tick box from appearing when you try to install the free version).
However you've no need to worry. Simply allow the PRO version to run out; it then automatically becomes the free version anyway. (Remember that the free version doesn't 'run in the background'; it doesn't do anything unless you actually run it from time to time).