In this paper, we present a simple method of fabricating the hot embossing tools using polydimethylsiloxane (PDMS). The tools are then used to fabricate microfluidic systems in polymethylmethacrylate (PMMA) of various aspect ratios. A negative photoepoxy (SU-8) or thick positive (AZ4620) photoresist on silicon is used as a molding template for the casting process to obtain a negative of the desired features in PDMS. The fabrication time of these PDMS tools is typically less and remains the same for realizing low as well as high aspect ratio features. This processing technique was used to fabricate microchannels over a wide range of aspect ratios in PMMA. This approach offers many advantages compared to the conventional methods of fabricating hot embossing tools including rapid processing, reduction in complexity and cost. This technique can also be extended to create orthogonal 3-D microfluidic systems in various thermoplastics.