Cutting out shapes

[Grale]

Ok i've worked out that if i use boolean subtract, i can cut out the shapes i want, but i have a problem that it sometimes leaves a mess after cutting, it seems if i adjust the position of the shape i am going to cut out, it sometimes makes a clean cut !

Here's a couple of pic's of the problem:

before:



After Messy:



Any ideas what i can do??

Thanks
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Firstly hi to all here

I have just started out learning to use ac3d, i am trying to model an airplane i have as a first project, it's a simple design as it has a flat profile fusealage, the only thing not flat are the wings!

Ok so i have searched, found a few answers to my question, but i am still stuggling to do what i want, which is cut out different shapes from my fusealage, here's a picture:


ok so i want to cut out the squarish looking box and leave a hole the same shape where the box used to be, there are many more shapes like this one from round,oval ect...


Any help would be much appreciated

Grale