HRTF implementation in matlab
Each HRIR is meant to represent the acoustic impulse response from an audio source at a specified angle (relative to the head) to the ear canal.  There is no such thing as a 3D signal, but if you want to simulate audio from a given azimuth and elevation angle, just convolve your audio source with the corresponding HRIR as follows:

left_channel = conv(audio_signal,hrir_left_az_elev)
right_channel = conv(audio_signal,hrir_right_az_elev)


In this case, I am using hrir_left_az_elev to signify the HRIR that corresponds to the left-ear impulse response to a sound event at azimuth angle az and elevation angle elev.  How you actually code this up will depend completely upon the format of your HRIR data.