The paper presents the programming and program verification on a 3-axis hybrid kinematics CNC machine for rapid prototyping using subtractive and additive processes. The original hybrid (parallel-serial) 3-axis O-X glide mechanism developed to build a rapid prototyping machine and multifunctional machine tools is presented. The paper analyzes the available programming software, which can be one of the standard CAD/CAM systems or a specialized CAM system, for subtractive processes, i.e. desktop milling. For the additive processes, the software for generating G code based on the STL file as well as the possibility of simulating the machine when working is considered. To verify the program, the simulation of material removal for subtractive processes as well as the simulation of material addition for additive processes were considered. The paper presents the prototype of a hybrid kinematics CNC machine and some of the results of testing with an open control system based on the LinuxCNC