Create 2D drawings from 3D Models, using layers with different colors

Hello,

          I am using Autocad 2012. I need to make some  2D execution drawings from a 3D model. I tried to use the following commands: flatshot, flatten &section plane. All of them are having bad results. From all this 3 commands the closer to my needs is the flatshot. But I am working with many layers which have different colors, so when I will generate the 2D views I need to see the same color as the layers have (each color is for a particular medium). 

            I am using this command without showing the obscured lines. 

            When I am generatic the isometric views with the flatshot I am seeing strange objects (UFO), is far away from the original model, you can see in the attachment.

             My questions are: It is possible to generate somehow 2D views (front views&isometric views) seeing the color which every element has, and it is possible to correct somehow those ugly isometric views ( the guys from autocad should do something with this, because when I am generatic a isometric view the 2d drawing that I recived is completely different from the 3D model !).

             I want to make the drawings using the 2D views, because the 3D Models are very big (50-60MB) and it is very hard to work with them!  

              Waiting for sugestions! 

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