Micro scribing of copper and aluminum thin films in air and underwater using Q-switched Nd3+:YAG laser has been described. Influence of deionized (DI) water level on the scribed micro channel depth and width has been studied for different wavelengths. Scribing was done by maintaining different levels of DI water at 1mm, 2 mm, 3 mm, 5 mm and 10mm. At 1 mm DI water level and laser pulse energy of 3 mJ, maximum ablation depth of 105 μm was achieved with both 355 nm and 532 nm wavelength for aluminum. Further, the depth achieved in DI water was 6 times greater than that in air for aluminum. On the other hand, for copper film, the depth attained with the laser ablation in DI water was 7 um as compared to 4 um in air for 1064 nm wavelength and 40 mJ of energy. In case of 355 nm and 532 nm the depth attained in air was higher than in DI water for copper. As the DI water level was increased, the depth reduced for both aluminum and copper. A comparative study of the results obtained in both underwater and air media revealed that aluminum can be machined more potently in DI water than in air. Further, theoretical modeling of the laser-material interaction in air as ambience has been discussed to estimate the recession rate by incorporating the laser ablation temperature measured using the laser induced breakdown spectroscopy technique.