A method for producing in a roll-to-roll process modules of thin film photovoltaic cells in a substrate film, the modules including the substrate with a photovoltaic layer inbetween a lower and upper electrode layer, by using an apparatus including a belt conveyor, and scribe and print stations arranged at respective positions along a transport direction of the belt conveyor to create an interconnection structure between the photovoltaic cells including an arrangement of structural elements having one or more conductive and isolating scribe lines and a conductive body connecting adjacent thin film photovoltaic cells. The method includes: creating by the processing stations, the interconnection structure in the moving substrate film; measuring the structural elements and determining parameters of each structural element; based on the parameters establishing a positioning error, associated with a functional defect; based on the error, correcting settings of one or more processing stations and/or the belt conveyor.