The invention pertains generally to the field of biology and particularly to techniques and apparatus for the synthesis and analysis of biopolymers using micro-arrays. The present invention provides improved apparatus and methods in defining the active array locations for each nucleotide-adding operation, enhancing accuracy, flexibility, speed and performance. The apparatus comprises a process chamber, a light source (e.g. laser), a scanning device and at least one sensor unit for detecting the light received. The sensor unit functions as a reference position and may be used for calibrating the light beam. The information for the sensor units is used to compensate.for offset drift, gain drift or loss of laser power. In addition, the present invention relates to the synthesis of biopolymers, e.g. DNA- sequences, peptides, carbohydrates and lipids, carried out using. a patterning process on an activated or chemically inert surface of asubstrate. Non-grid patters are claimed as a non-trivial extension of laser based pattern generation in arrays. Substrates comprising at least one channel and at least one biopolymer at a spatially selected region, which extends over the sides of the channel, are also claimed.