The ability to pattern different polymers in microfluidic channels is indispensable for the development of multifunctional, "lab-on-a-chip" devices. A simple method, based on the concept of selective filling, is described for introducing different polymers at defined locations in microfluidic channels. Selective filling is based on the difference in the free energy of filling between an open and a covered part of the channel. It is implemented by covering part of the channel, along its length, with a temporary poly(dimethylsiloxane) (PDMS) slab. Preferential filling is related to the contact angle of the liquid solution on the chip surface. An expression for the critical contact angle is derived, and its dependence on the geometry of the channel is established. It is further shown that a trapezoidal geometry of the cross-section of the channel is optimal for selective filling. Experimental verification of the applicability of the critical contact angle in predicting selective filling is demonstrated by introducing liquid prepolymer solutions of different contact angles in the glass channel that was etched using photolithography and wet etching. Finally, patterning of two different polymers along the axial direction of the microfluidic channel is demonstrated using this selective filling technique.