In this study the μ-rubbing technique is used to micro-pattern polyimide alignment layers using a metallic sphere at different loads. Optical and atomic force microscopy shows that the width of the patterns ranges from 12-40 μm and depth ranges from 2-14 nm. Our primary finding is that μ-rubbing induces planar alignment in polyimides. We performed μ-rubbing on pre-rubbed polyimide perpendicular to the rubbing direction. It is found that μ-rubbing erases the alignment properties of the pre-rubbing procedure. Liquid crystal cells were constructed using the pre-rubbed polyimide substrates with μ-rubbed patterns on one side and a homogeneously rubbed polyimide layer on the other side. Therefore the pre-rubbed polyimide layers are crossed and consequently a twisted nematic alignment is observed outside the micro-patterns. Within the micro-patterns, the directions of the pre-rubbing and μ-rubbing are parallel, a planar alignment observed. In another configuration, liquid crystal cells were made with pre-rubbed polyimide substrates having micro-patterns on both sides to give grid pattern with planar and twisted nematic configuration. Studies were extended to determine the pretilt of the micro patterned area.