Silicon heterojunction (SHJ) solar cells take advantage of the passivation properties of amorphous silicon: it can be easily doped, deposition temperatures are very low (below 200◦C), and it has very good passivation properties, but it has the drawback of very high sheet resistance for heterojunction emitters. An alternative to the use of a-Si:H in SHJ cells are transition metal oxide (TMO) films. These films have interesting properties as passivators and selective contacts for novel semiconductor devices, i.e. hole transport layers (HTL) or electron transport layers (ETL), and can be deposited on both electrodes of a solar cell. In this work, we present a complete study of the laser ablation of three transition metals that show good properties as p-type front contacts for n-type crystalline silicon heterojunction solar cells: WOx, VOx and MoOx. We characterize the ablation process of films deposited on crystalline silicon using laser sources of three different wavelengths (355 nm, 532 nm, and 1064 nm) and in two temporal regimes(picoseconds and nanoseconds). We measure the fluence threshold to remove the transition metal oxide (TMO) film and to induce the damage in the crystalline silicon substrate, determining the parametric window of the process. We also studied the morphology to analyze the relationships between crater dimensions and ablation parameters using confocal microscopy. Complete removal of the three different TMO films was achieved without damaging the silicon substrate. Results of diode isolation and their electrical characteristics are presented, showing the quality of the laser isolation processes.