The MagAO-X instrument is an upgrade of the Magellan AO system that will introduce extreme adaptive optics capabilities for high-contrast imaging at visible and near-infrared wavelengths. A central component of this system is a 2040-actuator microelectromechanical (MEMS) deformable mirror (DM) from Boston Micromachines Corp. (BMC) that will operate at 3.63 kHz for high-order wavefront control. Two additional DMs from ALPAO will perform low-order and non-common-path science-arm wavefront correction. The accuracy of the wavefront correction is limited by our ability to command these DMs to a desired shape, which requires a careful characterization of each DM surface. We have developed a characterization pipeline that uses a Zygo Verifire Interferometer to measure the surface response and a Karhunen-Loeve transform to remove noise from our measurements. We present our progress in the characterization process and the results of our pipeline applied to an ALPAO DM97 and a BMC Kilo-DM, demonstrating the ability to drive the DMs to a flat of ≤2nm and ≤4nm RMS in our beam footprint on the University of Arizona Wavefront Control (UAWFC) testbed.