nanoXplorer IDE makes the nanodevice design its central paradigm. To store information about these nanodevice designs, nanoXplorer IDE uses the NanoFile format, created by nanoTITAN. NanoFile's have the following attributes:

- NanoFiles use the ".nano" extension.
- NanoFiles are compressed zip files for excellent storage efficiency.
- NanoFiles include one nanoML file and any number of atomic system data (ASH5) files.