Open Pro Tools and insert the vocal version of the song into Track 1.
Insert an instrumental version of the song into Track 2.
Align both tracks so they are perfectly in sync.
Insert the EQ3 plug-in on the instrumental track and click the Phase Switch option. This essentially reverses the polarity of track. On the waveform, you will now see valleys where there were peaks and vice versa. The effect is a nullification of all signals in common between the two tracks. Because one track has vocals and the other doesn’t, however, the vocal will remain as it occupies a frequency range that is not affected by the phase inversion.
Bounce the project as a new track for your acapella version. From the main menu, click "File," then "Bounce to Disk." This opens a pop up box for you to choose your output settings. For this exercise, choose .wav as your file type, mono as your format, 16 bit as your resolution and 44.1 as your sample rate. This will give you a flexible CD quality rendering.
Open a new session in Pro Tools and insert your new acapella into Track 1.
Apply a noise gate to the track. From the main menu, click "Plugin," then click "Expander/Gate." Play the track while adjusting the gate and adjust the threshold to eliminate any lower volume “bleed” remaining from the instruments.
When adjusted properly, the gate will open only when the volume of the vocal exceeds the threshold you set. This allows you to clean up the track and remove any sounds occurring outside of the vocal parts. Each song is different, so you will have to rely on your ears to find the right threshold setting.