Highpass filter square wave Generated a 1kHz square wave in Audacity and normalized it to 0dB (fs = 44100Hz):

Added a 24dB/oct high pass filter (std Audacity plug-in), cutoff frequency set to 100Hz. Result:

Zoomed version:

Why &quot;clipping&quot; so badly?
EDIT: When normalized to -3dB before filtering there's no &quot;clipping&quot; present.
Filtering same signal with low pass filter does not have this issue.
That's perfectly normal and expected. You are removing harmonics and as a result you change the time domain wave form. There is no guarantee or expectations that the maximum amplitude will be maintained.
In fact, a square wave has the lowest possible Crest factor (ratio of peak to RMS) and ANY change will increase the Crest factor. In order to not clip you need to remove a substantial amount of power (which your lowpass probably does).