Either truncate your spectra (the command in Chemstation used to be MSTRUNC, not sure what it is in Masshunter) or change your acquisition parameters to limit the level at which the system will register a signal.

Thresholding will remove the lowest peaks. There are multiple ways to do this, but most require you to enter a threshold value which will be applied as a constant across the spectrum any peak below that threshold will be eliminated. There are ways to do dynamic thresholding with noise discrimination, but not in the vendors' software. See the below:

Method Mass Spectral Data Processing