Pulsed laser processing is a technique to induce optical and structural changes in materials, such as oxide line and ring structures, when metallic samples are irradiated with high intensity lasers in oxygen and mixed atmospheres. The oxides, which can have very different electrical and optical properties, are gaining momentum in novel technical applications such as electrochromic devices, electrodes in microbatteries, gas sensors, and catalysts, among others. When a femtosecond laser irradiates a transition metal thin film, the thin film reacts with the gaseous species, producing different chemical and structural phases, depending on the localized atmosphere and laser irradiance characteristics, e.g. the fluence, polarization, and duration of exposure. Here we present a processing study of femtosecond (fs) laser processing on molybdenum (Mo) thin films. The laser used is an Ytterbium-doped oscillator in the near infrared (1028 nm), ultrafast (230 fs pulse width), and with a high repetition rate (54 MHz). Irradiations are done under ambient air as well as pure oxygen gas conditions to document how the oxidations occur under varying environments. Our results indicate that the high heating rates and electric-fields associated with laser processing allow the production of different phases and that a detailed fine-tuning of different variables can manipulate the oxidation of the samples. Raman spectroscopy, scanning electron microscopy, and atomic force microscopy are used in characterizing the oxidation of the different phases for the different irradiation parameters chosen. Our results indicate a high correlation between the increasing of the alpha-MoO3 formation area with the increasing of gas concentration and pressure.