Files are commonly saved within a folder structure. You should consider whether one big-flat folder for all your files or a hierarchical tree structure would be the most appropriate for the piece of work or project you are doing. A complex structure can encourage the use of shorter less meaningful file names that are dependent on that structure. This may mean that when the folder structure is removed, for example when you provide your data to a collaborator, the file names may have little or no meaning. To avoid this try to use names that match your environment and contain:
Develop a system for file naming that works for your project or work, use it consistently and make sure it is part of the assigned metadata. The UK Data Archive has a useful guide for formatting your data.
Ideally all data items related to a project, with associated metadata, should be grouped, and deposited with a summary of contents and relationships, itself in an appropriate open format. You may want to consider using a database or spreadsheet to track data.
Data analysis software such as NVivo can be used to describe and document data.