Polylactide (PLA) and acrylonitrile/butadiene/styrene (ABS) are the most commonly used polymers for the additive manufacturing using fused filament fabrication. Additive manufacturing is commonly known as „3D printing“. In order to develop new materials for 3D printing of microreactors, these two polymers were blended with high-density polyethylene (PE-HD) and low-density polyethylene (PE-LD) under different process conditions in several ratios. Mechanical and thermal properties, as well as morphology of polymer blends are determined. In order to investigate the possibilities of designing hydrophobicity of polymer blends to gain more control over fluid flow inside microchannels of 3D printed microreactors polymer blends surfaces were etched using inductively coupled plasma (ICP) and coated by fluorocarbon-based material (CFx) plasma deposition treatment in the second step. The results obtained showed that the preparation temperature (160 °C vs. 180 °C) or the mixing equipment (extruder vs. kneader) of the polymer blends had no significant effects on the mechanical properties of the polymer blends. The greatest influence on the mechanical properties of polymer blends has the size distribution of the dispersed phase in the matrix. Better mechanical properties showed samples with a narrow size distribution of the dispersed phase domain that are uniformly distributed within the polymer matrix. Such specific morphology showed samples with PE-HD. Regarding the hydrophobicity, it has been shown that the surface morphology of PLA polymer blends can be highly modified by etching and CFx coating, while it was not possible for ABS polymer blends under the conducted treatment conditions. The treated surface of PLA/PE-HD 90/10 showed contact angle of 121.6° which is up to 36° higher than the contact angle measured on the untreated surface. Surfaces achieving high contact angles (> 120°) have “island like” surface morphology. Samples with higher "islands" showed higher contact angles, that confirmed that the hydrophobicity also depends on the height of the "islands". Furthermore, it has been revealed that the longer time of etching has significant impact on the contact angle values as well as surface morphology of the PLA polymer blends, while the longer time of CFx coating has no significant impact on the surface characteristics. Furthermore, it has been shown that filament for 3D printing can be made of PLA/PE-HD 90/10 polymer blend as well as 3D printed microreactor.