First we load the spectrum to be analyzed in TOPPView. If you want to test the described tools, you can open the tutorial data via the File-menu (File > Open example file, then select peakpicker_tutorial_1.mzML). The BaselineFilter can be called via the Tools-menu (Tools > Apply TOPP tool), then select BaselineFilter as TOPPtool (red rectangle). One can choose between different types of filters (green rectangle), the one mainly used is TopHat. The other important parameter is the length of the structuring element (blue rectangle). The default value is 3 Thomson. Press OK to start the baseline subtraction.

The following image shows a part of the spectrum after baseline filtering as green line, the original raw data is shown by the blue line.