Structure Editor supports two kinds of structure formats: MDL MOL-files (SDF-files), with the *.mol (*.sdf) extension, and HighChem MCS format (Maximal Compressed Structure), with the *.mcs extension. These formats are also supported in the Database Manager module. Templates are stored in MCS-format, using the extension *.tml.

One of Mass Frontier's particularly useful features is the ability to restrict a search by a set of structural constraints, the so called "Good-Bad" list. For example, you can instruct the program to conduct a library search comparing an unknown spectrum only with the spectra of ketons. This feature provides an endless range of possibilities to target your search results with. The “Good-Bad” structures are stored in the directory ..\Constraints, and the structures are saved in MSC-format (*.mcs). The program automatically retrieves all MCS-structures from ..\Constraints directory and puts them in a “Good-Bad” list box in the Constraints dialog box.