I have a SER # 2 aluminum XHHW insulation, three wires each plus a ground, since I do not need the bare wire for my hook up, will I be violating any NEC

The bare wire in this cable is the ground. You DO need it.

Why not tell us what the circuit is for so we can assist you further?

I will be using the cable to replace a dilapidated SER Alum (THHW) Cable for a 100amp service 2-phase connection from the Base Meter to the Electrical Panel, above ground. The old cable has 2 insulated conductors and one bare twisted wire. My question is, I have a new cable that has 3 insolated wire 2 hot, 1 neutral and 1 bare ground = 4 conductors however all I need is 3 conductors for my service connection, my plan is to cut the bare wire flush with the insulation and only use the 3 that I need for my hook up. Is this allowed or will it fail inspection?

I'd have to search for the code, but I think it would fail.

How much could you need? Just because you have it does not justify using it IMO.
Just get the proper SEU cable.