How to create a very accurate STL file as well as the slices for a 3D printer? I have been using Solidworks and AutoCAD to create STL file of a 3D model I want to print. I slice the STL file using Freesteel Z level slicer (http://www.freesteel.co.uk/wpblog/slicer/) and save the slices in a bmp format. 

My 3d print has an array of circular channels, all of one radius. I expected the bmp slice to contain the circular shapes looking exactly identical to each other. However, I don't obtain the exact same replicas. Looks like the pixel-wise mapping has not been done uniformly. (View http://s24.postimg.org/p7w09zvkl/snippet.png for the image). 

I want each and every circle to be represented by exactly the same set of pixels in the bmp image, so that all of the circular contours are identical. (I do not prefer changing the pixel resolution.)

How can I overcome this problem? Are there any better tools which would lead to a perfectly uniform pixel-wise mapping? 

Thanks! 

PJ
Your objective has a serious constraint regarding the pixel resolution. Within that limitation, the software (slicer) you are using will generate "best guess" images, particularly dependent on floating point math. There may be a single combination of circular shapes (radius) and spacing for these shapes that provides your objective, but that's likely not a practical exercise.

You have not indicated if you've tried other slicers, which would be the primary direction. A list of choices can be found here:

Free Slicing Program List

Another option that you can consider, not included in this list, is to use OpenSCAD, import the STL file, then use the projection() command to manually slice and export the image file. I use the term "manually" but the program can be coded to perform this task automatically, and there is a command line feature to OpenSCAD that may be useful.

Note also that the output of these slicers and/or OpenSCAD may exceed the resolution you desire. Manipulation of the image with a graphics editor could result in the same floating point disarray as you perform the changes.