With the exception of modes, presently we can only detect antimatter in our apparatus by destructive methods (we either need to splat our particles onto a detector surface or annihilate the antimatter into the trap wall). While working with antimatter makes almost everything very difficult, fortunately detection is often very efficient.
We either detect the charge of particles in our apparatus (Faraday Cup, MCP, temperature measurements), or the annihilation products. When antimatter comes in contact with matter, it annihilates. This annihilation releases lots of energy and subatomic particles. These products are then detected either with the Plastic Scintillators, TPC, SVD.