Yes there is, but it is a bit of a nuisance to program, as it involves operating-system specific operations that are not supported by MATLAB (POSIX pipe() or MS Windows _pipe()). This interface would have to be coded in a MEX routine.
The complete I/O stream for talking to the other process would have to be coded in MEX, as the MATLAB I/O streams offer no way to flush an I/O buffer and no way to pass a MATLAB I/O stream to a MEX routine (so you can't have C do it for you.)
I notice you reference plink.exe which tends to imply you are on MS Windows. In MS Windows only, if there is a DCOM / ActiveX control to ClearCase then you can use MATLAB's activex() call to open a session.