Prototyping microfluidic devices using laboratory based methods, such as PDMS casting, is faced with barriers for commercialization, because of differences of material properties, scale-up capability, bonding and surface treatment, etc. Using commercially available plastics for prototyping offers benefits of more direct process transfer and medium to mass production capability. In the present work, a flexible mould was designed, which can fabricate both a polymer microfluidic chip and cover in one single mould by using exchangeable inserts. Prototyping of polymer microfluidics using COC 8007 has been demonstrated using various tool inserts manufactured using either Stavax stainless steel or electroplated Ni. Replication of multi-scale features and surface roughness has been compared for different tools.