Facioscapulohumeral muscle dystrophy (FSHD) is the third most common muscle disease in the world. No cure has been found for FSHD, and current treatments focus on alleviating the symptoms. The disease is caused by a genetic error in 1/1000 - 1/200 of the nuclei in a multinucleated skeletal muscle cell. Studying that specific nucleus, by removing it from the cell, perform transcriptomics on it and determining the cell viability after the nucleus removal, can provide important information about FSHD. In this work, a multiscale 3D printing approach was optimized to fabricate a microfluidic atomic force microscopy (AFM) cantilever that can remove a nucleus from a living cell. With the device mounted on an AFM system, cell experiments were performed, which showed that the nucleus can be removed from a cell using 3D printed microfluidic cantilevers. The printing methods can be used to fabricate various types of suspended microfluidic devices to perform single-cell biopsy and biophysical characterization of single-cells.