How to remove the artefacts of an electrogram signal?

I am getting electrogram recordings using a micro-electrode arrays system on cell cultures. When I analyse my electrograms on Matlab, I have usually big artefacts at the stimulation points - they're steep like the R peak - and they cause problems sometimes at the peak-to-peak detection, because I use 'MinPeakHeight' from the Signal Processing Toolbox. That's because it happens sometimes the electrograms to be shorter than the artefact. They're not always at the same locations. Could you please advice me how it'd be better to filter them? Thanks.