Micro-pillars forming in micro channels have been implemented by hot embossing. With dry etching and chrome photo mask, the silicon mold was fabricated using lithography process for manufacturing micro-pillars in micro channels. The hot embossing experiments are executed on the embossing machine by embossing the PMMA substrate and the silicon mold. Making the polymer filling in the concave cavity of the silicon mold is a difficulty, so the laws of polymer filling in the concave cavity were researched. The effects of three key embossing parameters including pressure, temperature and time on the PMMA replication accuracy were studied, and the optimal molding parameters were obtained. This work is instructive to fabricate microfluidic chips with micro-pillars.