The geometric designs of MEMS devices can profoundly impact their physical properties and eventual performances. However, it is challenging for researchers to rationally consider a large number of possible designs, as it would be very time- and resource-consuming to study all these cases using numerical simulation. In this paper, we report the use of deep learning techniques to accelerate the MEMS design cycle by quickly and accurately predicting the physical properties of numerous design candidates with vastly different geometric features. Design candidates are represented in a nonparameterized, topologically unconstrained form using pixelated black-and-white images. After sufficient training, a deep neural network can quickly calculate the physical properties of interest with good accuracy without using conventional numerical tools such as finite element analysis. As an example, we apply our deep learning approach in the prediction of the modal frequency and quality factor of disk-shaped microscale resonators. With reasonable training, our deep learning neural network becomes a high-speed, high-accuracy calculator: it can identify the flexural mode frequency and the quality factor 4.6 × 10³ times and 2.6 × 10⁴ times faster, respectively, than conventional numerical simulation packages, with good accuracies of 98.8 ± 1.6% and 96.8 ± 3.1%, respectively. When simultaneously predicting the frequency and the quality factor, up to ~96.0% of the total computation time can be saved during the design process. The proposed technique can rapidly screen over thousands of design candidates and promotes experience-free and data-driven MEMS structural designs.