You can restrict the tracker to either track or not track specific applications, web sites or documents. To make the changes, open Settings, then go to Tracking.

Restrict tracking by applications, web sites or documents

You can restrict by just checking items on the right side. At the top you can choose whether selected applications should be tracked or if it should track everything else except selected applications.

Restrict tracking by applications, web sites or documents

You can also type by hand. For example if I wanted to not track time I spend in Notepad, I could just write "notepad".

Don't track any Notepad usage

Notice that it also includes usage of Notepad++ and Notepad2. If I want to only exclude Notepad.exe usage, I can surround the text in double quotes.

Don't track any Notepad.exe usage

Restrict tracker to not track when specific words are in window title
                 
I guess the best example is to not track any porn sites. Of course we never look at that stuff, but if we did, here is how we would keep it from registering in ManicTime.

Please, don't track my porn...