Pure molybdenum, titanium - zirconium - molybdenum (TZM) and molybdenum - hafnium - carbon (MHC) are among the most industrially used molybdenum based materials. Although there are many applications areas of these materials, they are mainly used in defence and aerospace industries. Finishing cuts are among the critical machining operations because of the requirements of high surface quality and dimensional accuracy. Due to the requirements of high surface quality and high dimensional accuracy, it is important to determine and optimise finishing cut parameters beforehand. For this reason, it is necessary to determine the machining parameters such as cutting speed, feed rate, depth of cut and cutting tool material and geometry. In this study, it is aimed to determine the optimum cutting tools and cutting parameters in terms of average surface roughness (Ra) and cutting forces (Fc) in milling of three different molybdenum based materials. The milling test design was accomplished using Taguchi’s L16 orthogonal arrays. An analysis of variance (ANOVA) was also employed to determine the level of the effect of control factors for the main cutting force (Fc) and average surface roughness (Ra). By using the signal/noise ratios, the optimum values of the control factors were found to be at different levels for the cutting forces and average surface roughness. The ANOVA analysis showed that the feed rate was the most significant parameter for the cutting forces while the cutting speed was the most significant parameter for the surface roughness.