Here you need to know before CIFOUT.

Ensure all of the layout objects are located at the first quadrant of the cellview as shown below,
If layout containing instances (sub-cells) with magnification other than 1. Those instance must be flattened.
Since the pattern transferred to the wafer is a MIRROR image of the mask pattern. Therefore, if you want to have pattern exactly equal to the layout pattern on the wafer, the existing layout should be mirrored.
To mirror your current layout, create a new cell and its cell view. Then open this cell view and select Create->Instance. In the instance form, enter the library name, cell name and view name. Click on "Sideways" and then choose OK.
Then select Edit->Other->Flatten to flatten the object created by Instance. A mirror image of your original layout is created.
To make sure the translation program can reconginize the actual size of your chip, you should put small squares (eg, 1um x 1um) at both botton left and top-right corner of your chip for those layers without patterns in these areas.
Also, the layout size in Y direction should be in multiple of 256um. You may create the small square in upper-right to the proper location.
You should create seperate output file by CIF Out for each layer of your layout. (i.e. The number of output files equals the number of layers)