"user enter a variable size matrix": It depends on how you want to implement this: by a GUI, as Matlab code, as text file, in Excel?
"another for the plain text": Of course a text file would be my first idea. But a GUI with an edit field would be sufficient also.
"how could I convert the letters into certain numbers": Simply by using the double() command, which converts the characters to their ASCII codes.
"fill the array with null operators": What is a "null operator"? I guess simply using zeros might be fair.