You can save an assembly so that you can work on it at a later date, or you can save the reference sequence as a single MacVector sequence.
Choose Save or Save As... from the Edit menu - the default format is set to MacVector Assembly. Type or select a file name then click Save to save the assembly.
MacVector uses BSML, an XML-based format to save the assembly. This is a text format that is used by other applications such as DS Gene. These files can get fairly large if you have an assembly with a lot of trace files because all of the data from each chromatogram is stored in the file. Expect a typical assembly of 30 traces to generate a file of ~2.5MB.
If you have made changes to the reference sequence, you may want to save this as a normal MacVector sequence so that you can use it in other analyses and have a definitive copy of the sequence of your clone.
Choose Save As... from the Edit menu and then select MacVector Single Nucleic Acid Sequence from the Format popup menu. This will save the reference sequence and all features into a standard MacVector format file. Although the actual residues of the assembled sample sequences are not included in the file, their names and locations are saved as Read features as a reminder of the files you used to create the assembly.