Question: I have a noise completely correlated with the laser trigger that screens the signal for low intensities. The noise is always the same and just removing it from the data I retrieve the signal. Do you know how to avoid this noise?

This is a pickup, not really a noise. It is very small as you noticed and depends on environment,i.e. grounding, shielding. Simply take a waveform a substract it from the rest of the waveforms.