optical scanner system approaches are described in which novel focusing approaches are provided . a control algorithm accounts for geometric variation of successive scans in opposite directions across a microarray slide or substrate in order to provide optimized focus . the feedback approach taught may involve pi or pid terms . in either type of control approach , a projected slope of the slide is calculated and followed back and forth outside a scan region of the array in exiting and entering fully adaptive focusing zones , respectively . during turn - around , the system may track a setpoint between the periods of following the extrapolated slope . also provided are methods of using the subject system in a biopolymer array based application , including genomic and proteomic applications .