There are many rules that determine if Boolean's work or not. All I can say based on the data you have provided is that you must be breaking some rule(s) or the Boolean would be working. With the info you have provided I have no way of knowing what you are doing wrong. You might want to provide some screen captures. Attached is screen shot of what I am working on. It's the low poly character tutorial offered on this site. The geometry is intersecting so I am not sure why it won't work.