CIF (Caltech Intermediate Format) is used as an interchange between design systems and fabrication facilities. CIF options are controlled with the "CIF" preferences (in menu File / Preferences..., "I/O" section, "CIF" tab).
This dialog controls the conversion between layers in Electric and layers in the CIF file. By clicking on an Electric layer, you can type a new CIF layer into the dialog.
By default, CIF output writes the entire hierarchy below the current cell. If you check the "Output Mimics Display" item, cell instances that are unexpanded will be represented as an outline in the CIF file. This is useful when the CIF output is intended for hardcopy display, and only the screen contents is desired.
Another option is whether or not to merge adjoining geometry. This is an issue because of the duplication and overlap that occurs wherever arcs and nodes meet. The default action is to write each node and arc individually. This makes the file larger because of redundant box information, however it is faster to generate and uses simpler constructs. If you check the "Output Merges Boxes" item, all connecting regions on the same layer are merged into one complex polygon. This requires more processing, produces a smaller file, and generates more complex constructs.
Another option is whether or not to instantiate the circuit in the CIF. By default, the currently displayed cell becomes the top level of the CIF file, and is instantiated at the end of the CIF. This causes the CIF file to display the current cell. If the CIF file is to be used as a library, with no current cell, then uncheck the "Output Instantiates Top Level" checkbox, and there will be no invocation of the current cell.
When reading CIF files, the CIF "wire" statements are assumed to have rounded geometry at the ends and corners. If you check the "Input Squares Wires" item, CIF input assumes that wire ends are square and extend by half of their width.
You can request that resolution errors be checked during CIF output by checking "Find resolution errors". The "Output resolution" field is the minimum coordinate value that can be safely written in CIF (due to CIF's use of the centimicron as the smallest unit). All geometry of that size or less will be flagged during CIF output. For example, current MOSIS rules require that no boundaries be quarter-lambda or less, so a value of .25 in this field will detect such violations.