Read the FAQ: http://matlab.wikia.com/wiki/FAQ#What_is_the_path_in_my_deployed_application.3F. Sorry, I know it's complicated but that's the way it is.
It's a lot more complicated than just saying ctfroot. ctfroot is not where your executable is. And the "current" folder is not necessarily where your executable is, or where ctfroot is, or where matlabroot is. There are a bunch of folders, some/most of which I go over in the attached demo. Read over the attached file's comments. Then compile the application and put the created executable somewhere (in some folder where you want it to be installed). Then run it and find out some things, some of which are surprising.
There are also some things you will learn in there about shipping files with your app - where they need to go and how you need to refer to them (their filename) to access them.
