This report presents a multilevel microfluidic platform for robust construction of hydrogel scaffold in microchannels and its application to three dimensional (3D) multicellular co-cultures and assays. A new rapid prototyping method based on soft lithography using multi-layered adhesive tapes is also introduced. We have successfully cultured MCF-7 breast cancer cell line more than 11 days with > 98 % viability, and co-cultured MDA-MB-231 breast cancer cells and NIH/3T3 fibroblasts in separate compartments. This multilevel microfluidic device with a cell-laden hydrogel microstructure has also been applied for anticancer drug assays in multicellular niches. Here we tested the effect of estrogen receptor (ER) antagonist drug, tamoxifen, on the growth of ER positive MCF-7 cells in microchannels. The inhibitory effect of tamoxifen on the growth of MCF-7 cells was diminished when they were co-cultured with ER negative MDA-MB-231 cells. The rapid prototyped multilevel microfluidic devices would provide simple, easy to use, low cost, robust, and reproducible cell-based assay platforms for potential end-users such as biologists and pharmacists.