Mindboards

I am building a plant watering robot using anthropomorphic arm manipulator, I am programming it in SIMULINK and MATLAB.

I need help on how to define reference trajectories for the arm manipulator which are going to be fed into my controller as the reference input. My idea is to build it to be in a fixed position with 3 RC motors. Motor 1 rotates only around z axis and it should stop rotating as soon as any plant is detected by the ultrasonic sensor installed on the first link which is along z axis.
Motors 2 and 3 are used to move links 2 and 3 to drive the end-effector exactly on top of the detected plant and then move it down toward the plant and water it afterwards and return back after completing the task.

Wow, this makes me feel highly unintelligent. If you can re-state that in plain English, I might understand what you're asking, and it sounds like something I'd love to help with.

He's using fancy speak for saying he's making a robot arm that waters plants

As for calculating trajectories, you need to tell us what the arm looks like, dimensions, etc. You need to look into Inverse Kinematics, which, unfortunately, is way above my paltry math skills. Will your motors have encoders of some kind? what do you mean by "RC motors"?

- Xander