Template:WinePrefix
When you run Wine it will create a basic Windows system by default in $HOME/.wine. That is called a "Wine prefix". While it's fine to leave it like that, you can run each Windows program in its own Wine prefix, so that you can easily and cleanly remove all traces of one program without affecting the others. For example you might keep Adobe DNG Converter in its own Wine prefix in $HOME/wine-dng and decide to try out some proprietary Windows HDR program. You might find out that you don't like this program, or that the trial period has expired, or that it simply doesn't work. Uninstalling it, if the uninstaller even works, is known to leave things behind. If, on the other hand, you installed this program to its own Wine prefix, say $HOME/wine-hdr, you could simply delete that folder and that program would be gone without a trace, without affecting Adobe DNG Converter.
Creating a new Wine prefix is very simple. All you have to do is to prepend WINEPREFIX="$HOME/some-folder" before the wine command. If that folder does not exist, Wine will create it for you. It is a good idea to double-quote the path. For instance, WINEPREFIX="$HOME/wine-hdr" wine