In MATLAB documentation I can the see the clean morphological operation here. The issue is that I'm not able to use it. I know how to use the structured element, but if I for instance type imclean(img,SE) or clean(img,SE), I get an error as an undefined function. How should the function be used?
There are no functions called clean or imclean in Matlab.
Matlab has a general morphology function for binary images (bwmorph) that takes strings as input for what operation to perform. So what you want to do is
bwmorph(img,'clean')
(This is based on R2013b - but this holds for other recent versions too AFAIK)