Output of KISS FFT interpretation
What you might want to investigate is FFT fast convolution using overlap-add or overlap-save methods. You will need to expand the length of each FFT by the length of the impulse of your desired filter. This is because (1) FFT/IFFT convolution is circular, and (2) each index in the FFT array result corresponds to almost all frequencies (a Sinc shaped response), not just one (even if mostly concentrated near one), so any single bin modification will leak throughout the entire frequency response (except certain exact periodic frequencies).