We present an experimental protocol for fabricating enclosed microfluidic channels using polymethylglutarimide (PMGI). PMGI is optically transparent, biocompatible, and can be used to readily fabricate micrometer-scale lateral and vertical dimension channels using conventional photolithography. The low auto-fluorescence intensity of PMGI facilitates imaging of analytes without interference. The hydrophilicity of PMGI allows fluid exchange in micrometer-scale channels using a hydrogel as an interface without an external pump. As a demonstration, we assemble fluorescently-labeled lipid bilayers in PMGI microfluidic channels and show that PMGI has negligible auto-fluorescence intensity compared to the lipid bilayer. PMGI channels together with hydrogel-assisted fluidic exchange provides a simple approach to fabricate micrometer and sub-micrometer scale fluidic channels for optofluidics, molecular biology, and other medical diagnostic and sensing applications.