You may want to use cwd in your program, then use system(). Beware of the fact that on most systems (and i suspect Win32 too) system() opens a new shell for each call. So, your first would chage directory and then close, and your second would delete files in the current directory.

As a side note, if you are deleteing files you may want to look at unlink, which will let you check the status of your deletes. (glob + unlink = gooood)