Differential activation of neuronal populations can improve the efficacy of clinical devices such as sensory or cortical prostheses. Improving stimulus specificity will facilitate targeted neuronal activation to convey biologically realistic percepts. In order to deliver more complex stimuli to a neuronal population, stimulus optimization techniques must be developed that will enable a single electrode to activate subpopulations of neurons. However, determining the stimulus needed to evoke targeted neuronal activity is challenging. To find the most selective waveform for a particular population, we apply an optimization-based search routine, Powell’s conjugate direction method, to systematically search the stimulus waveform space. This routine utilizes a 1-D sigmoid activation model and a 2-D strength⁻duration curve to measure neuronal activation throughout the stimulus waveform space. We implement our search routine in both an experimental study and a simulation study to characterize potential stimulus-evoked populations and the associated selective stimulus waveform spaces. We found that for a population of five neurons, seven distinct sub-populations could be activated. The stimulus waveform space and evoked neuronal activation curves vary with each new combination of neuronal culture and electrode array, resulting in a unique selectivity space. The method presented here can be used to efficiently uncover the selectivity space, focusing experiments in regions with the desired activation pattern.