An advanced control system is considered for wood Thermal Treatment Processing (TTP) in order to cope with the scarcity of on-line measurements as well as cope with a variety of unpredictable operational conditions arising due to disturbances and large uncertainties. The architecture of the proposed control system includes a number of Building Blocks (BB), functionally based on well-established algorithms, so that that the design and operation of the system use mainly parameterisation via simulation, optimization and coordination. In the created BB a set of advances are incorporated: first principle modelling of WEP, inference control, Run-to-Run optimization, Case-Based Reasoning (CBR). Some results of real applications in SMEs are presented.