The microstrip devices based on multimode resonators represent a class of electromagnetic microwave devices, promising use in tropospheric communication, radar, and navigation systems. The design of wideband bandpass filters, diplexers, and multiplexers with required frequency-selective properties, i.e., bandpass filters, is a complex problem, as electrodynamic modeling is a time-consuming and computationally intensive process. Various planar microstrip resonator topologies can be developed, differing in their topology type, and the search for high-quality structures with unique frequency-selective properties is an important research direction. In this study, we propose an approach for performing an automated search for multimode resonators’ conductor topology parameters using a combination of evolutionary computation approach and surrogate modeling. In particular, a variant of differential evolution optimizer is applied, and the model of the target function landscape is built using Gaussian processes. At every iteration of the algorithm, the model is used to search for new high-quality solutions. In addition, a general approach for target function formulation is presented and applied in the proposed approach. The experiments with two microwave filters have demonstrated that the proposed algorithm is capable of solving the problem of tuning two types of topologies, namely three-mode resonators and six-mode resonators, to the required parameters, and the application of surrogated-assisted algorithm has significantly improved overall performance.