Brain stimulation has the potential to create desired neural population activity states. However, it is challenging to search the large space of stimulation parameters, for example, selecting which subset of electrodes to be used for stimulation. In this scenario, creating a model that maps the configuration of stimulation parameters to the brain’s response can be beneficial. Training such an expansive model usually requires more stimulation-response samples than can be collected in a given experimental session. Furthermore, changes in the properties of the recorded activity over time can make it challenging to merge stimulation-response samples across sessions. To address these challenges, we propose MiSO (MicroStimulation Optimization), a closed-loop stimulation framework to drive neural population activity toward specified states by optimizing over a large stimulation parameter space. MiSO consists of three key components: 1) a neural activity alignment method to merge stimulation-response samples across sessions, 2) a statistical model trained on the merged samples to predict the brain's response to untested stimulation parameter configurations, and 3) an online optimization algorithm to adaptively update the stimulation parameter configuration based on the model's predictions. In this study, we implemented MiSO with a factor analysis (FA) based alignment method, a convolutional neural network (CNN), and an epsilon greedy optimization algorithm. We tested MiSO in closed-loop experiments using electrical microstimulation in the prefrontal cortex of a non-human primate. Guided by the CNN predictions, MiSO successfully searched amongst thousands of stimulation parameter configurations to drive the neural population activity toward specified states. More broadly, MiSO increases the clinical viability of neuromodulation technologies by enabling the use of many-fold larger stimulation parameter spaces.