Without a specially written program you are likely to run into the problem that the Arduino resets (and takes time to do so) when the PC application opens the serial port. Most operating system utilities can't deal with that.
I am not familiar with C# but it would not be difficult to write a short Python program that could be called from the command line and which would have the smarts to deal properly with the Arduino.
This Python - Arduino demo may give you some ideas. I believe it will work on Windows if you change the serial port references.
...R