The paper is devoted to comparing the features of the formation of oxide microstructures during direct laser writing on thin (100 nm) zirconium films deposited on glass and fused silica substrates to identify the most stable and predicted writing modes. The presence of self-induced oxide quasiperiodic structures was detected during continuous laser writing on zirconium films deposited on glass substrates. The effect of the formation of nanostructures, which are parallel cracks in the oxide layer and have a period equal to the recording step (250-500 nm), formed during the writing process on zirconium films deposited on a quartz substrate is revealed. The advantages of fused silica as a substrate material for direct laser writing on zirconium films are shown due to the higher softening temperature of fused silica compared to glass.