Laser ablation ionization mass spectrometry studies on polished surface structures of hard, high melting point multicomponent interconnect structures using our femtosecond-laser time-of-flight mass spectrometer have previously been proven capable of providing spatially resolved chemical depth profile data at the micro- and nanometer level. Transfer of experimental protocols tailored to suit such type of samples to low melting point materials with high surface roughness, however, is highly challenging, as thermal effects caused by interactions of the laser light with the targeted surface play a severe role in the latter case and may significantly deteriorate the analysis outcome. In this contribution we present a dedicated and detailed comparison of the distinct effects of near infrared and ultraviolet irradiation on the ablation process in femtosecond laser ablation ionization mass spectrometry studies on low melting point materials. As model substrate we use high surface roughness, as-deposited SnAg solder alloy, a material of major industrial relevance in microchip fabrication. We will demonstrate herein that polydimethylsiloxane replica casting is possible also from granularly structured, high surface roughness samples. Characterization of the laser ablation craters as well as of their polydimethylsiloxane replicas is carried out by mass spectrometric analysis, Scanning Electron Microscopy imaging, and furthermore, as a novel approach for this purpose, by white light interferometry. Integration of all obtained results significantly adds to the detailed understanding of laser ablation processes on low melting point, high surface roughness materials and allows identifying optimal depth profiling conditions for these demanding samples.