Rapid manufacturing of functionalized polymers enable a cost-efficient method for many applications in the biological, and medical sector. Laser structuring techniques differ for fast fabrication processes of thermoplastics. Here we report on direct UV laser ablation of polystyrene and polydimethylsiloxane to control wettability and bio-compatibility. For this purpose contact angle measurements and L929 cell growth experiments were performed as function of laser and process parameters. This work also describes the potential of laser-assisted hot embossing which has been introduced to replicate prefabricated micro- and nano-sized structures onto polymers proving it to be a cost-efficient and flexible method for surface functionalization. Therefore, pre-fabricated laser-induced periodic surface structures have been manufactured as mould inserts using ultrafast laser radiation near the ablation threshold. These mould inserts can also be made of nickel, silicon or glass proving laser-assisted hot embossing to be a versatile tool for the functionalization of thermoplastics and meet the requirements for modern manufacturing with regard to quality and production flexibility.