I'm not sure I understand you fully, but this is what I think you mean:
You have a single layer 2 network, basically a bunch of servers (and possibly other hosts) connected to a switch or series of switches that are not split into vlans. On this L2 network you have configured multiple subnets, so for example you have a server whose address is 192.168.1.100/24 and another that is 172.16.0.200.
Now you want to change things, such that each server actually sits on a separate vlan and can reach the other hosts only through pfsense.
Am I close? Can you provide a diagram of how things are and how you want them to be? You can do this for free on gliffy.com.