In a method for controlling the positioning of patterns on a substrate in a manufacturing process at least one registration measurement is conducted with a registration tool on at least one pattern formed in at least one layer on the substrate by a previous process step of the manufacturing process. From the registration measurement a position of the at least one pattern in a coordinate system is determined. The determined position of the at least one pattern is fed into an automatic process control of a manufacturing system for controlling a setup of the manufacturing system for a subsequent process step of the manufacturing process. The manufacturing process may be a wafer manufacturing process with a silicon substrate. Complementary information may be collected in addition to performing the registration measurement and fed to the automatic process control. The process steps may for example include lithography steps, etching steps, layer deposition.