The control of layer thickness and phase structure in two-dimensional transition metal dichalcogenides (2D TMDCs) like MoTe2 has recently gained much attention due to their broad applications in nanoelectronics and nanophotonics. Continuous-wave laser-based thermal treatment has been demonstrated to realize layer thinning and phase engineering in MoTe2, but requires long heating time and is largely influenced by the thermal dissipation of the substrate. The ultrafast laser produces a different response but is yet to be explored. In this work, we report the nonlinear optical interactions between MoTe2 crystals and femtosecond (fs) laser, where we have realized the nonlinear optical characterization, precise layer thinning, and phase transition in MoTe2 using a single fs laser platform. By using the fs laser with a low fluence as an excitation light source, we observe the strong nonlinear optical signals of second-harmonic generation and four-wave mixing in MoTe2, which can be used to identify the odd-even layers and layer numbers, respectively. With increasing the laser fluence to the ablation threshold (Fth), we achieve layer-by-layer removal of MoTe2, while 2H-to-1T' phase transition occurs with a higher laser fluence (2Fth to 3Fth). Moreover, we obtain highly ordered subwavelength nanoripples on both the thick and few-layer MoTe2 with a controlled fluence, which can be attributed to the fs laser-induced reorganization of the molten plasma. Our study provides a simple and efficient ultrafast laser-based approach capable of characterizing the structures and modifying the physical properties of 2D TMDCs.