If all three IAPs are in the same Vlan they are in the same "Group". The Virtual Controller (VC) is the Master of the group and pushes a copy of its' config to members of the group. As such, if you have three SSIDs configured on the VC all three IAPs will advertise the three SSIDs.
The only way to change this is to have three separate VCs -- each configured with only one SSID.
To have three separate VCs you have two choices:
1. They need to be connected, via Ethernet, to their own separate Vlans.
2. Alternatively, they could all be in the same vlan (wired via Eth); however, you must enable "Standalone Mode" on each of the IAPs so they all come up as their own VC.
They will not be able to connect via Mesh as they will, again, be in one group.
For more information please download the IAP 6.1.3.4_3.1.0.0 User's Guide - Ch.6 - Managing IAPs.