The future of machine tools will be dominated by highly flexible and interconnected systems, in order to achieve the required productivity, accuracy, and reliability. Nowadays, distortion and vibration problems are easily solved in labs for the most common machining operations by using models based on the equations describing the physical laws of the machining processes; however, additional efforts are needed to overcome the gap between scientific research and real manufacturing problems. In fact, there is an increasing interest in developing simulation packages based on “deep-knowledge and models” that aid machine designers, production engineers, or machinists to get the most out of the machine-tools. This article proposes a methodology to reduce problems in machining by means of a simulation utility, which uses the main variables of the system and process as input data, and generates results that help in the proper decision-making and machining plan. Direct benefits can be found in (a) the fixture/clamping optimal design; (b) the machine tool configuration; (c) the definition of chatter-free optimum cutting conditions and (d) the right programming of cutting toolpaths at the Computer Aided Manufacturing (CAM) stage. The information and knowledge-based approach showed successful results in several local manufacturing companies and are explained in the paper.