So far the desktop manufacturing is mainly done as islands of process modules or in some seldom cases the desktop factory is created in form of manufacturing line. Tampere University of Technology has been working on such desktop factory concepts for years and come out a microFactory concept (TUT-μF). The paper discusses architectural aspects and proposes some solutions for them. It specifies also two main mechatronic interfaces used for such modular desktop factories - 1) the cell to cell interface and 2) cell internal process module interface. Main parts of the specifications are represented. These can be utilised for building the desktop production line from easily integrated modules.