"The output I am getting is in 3x1 tf format" - This is correct because as per definition 'pid' command creates a continuous-time pid controller in parallel form. Basically you get a transfer function as a controller. When you multiply a constant (your input) to this transfer function, you get another transfer function.
"I need it to be 3x1 double at a single time instant"- One way is to convert the output from s domain to time domain using ilaplace or you can use the file exchange function given here. You will get your outputs as function of time from which you can easily substitute and get value of outputs at a particular time instant.
