The development of bulk metallic glasses for biomedical applications has become the focus of intense research interest. In this work, we report on the unique thermoplastic behavior of two Ni-free Ti-based bulk metallic glasses by utilizing the dramatic softening of the amorphous structure in the super cooled liquid region. Ti40Zr10Cu34Pd14Ga2 and Ti40Zr10Cu34Pd14Sn2 bulk glassy alloys were produced by copper mold casting. Ga and Sn micro-alloying (2 at%) improve the glass-forming ability and mechanical properties of Ti40Zr10Cu36Pd14 alloy effectively. The cast rods were thermo-mechanically characterized to determine the most suitable processing temperature and time, and the load that has to be applied for thermoplastic net-shaping of the BMGs into anisotropically etched cavities of silicon chips. Periodic features with high surface smoothness and uniform height (24 μm high circular bumps with sub-μm roughness) were created on the surface of the BMGs. The surface patterning with controllable roughness of Ti-based BMGs can be useful in biomedical studies by mediating material - cell interactions.