Good file management can help you in a variety of ways--from carrying out a more efficient research process to supporting future attempts to validate and replicate your research. You'll also want to be able to document your file management practices in your data management plan. Best practices for file naming and management include (with thanks to the Cornell Research Data Management Service Group for specific examples):
Document file-naming conventions and be consistent
Do not rely on the file directory structure to distinguish files
Avoid spaces, special characters, and periods in file names.
Use Electronic Lab Notebooks or Box to assign version control numbers. Use a system like Git to handle version control.
Avoid ambiguous labels like “final” or “revision.” Use a file-naming convention (like v01, v02, v1_0, v2_0, etc.).
Use version numbers, consistent dates, project names, and/or research initials in file names.
Use leading zeroes to facilitate sorting of files (i.e. 001, 002, etc.).
For bulk renaming of files, try a program like Bulk Rename Utility (Windows), Name Changer (Mac), Renamer (Mac).
This file naming example comes from Penn State Libraries. It shows proper use of the ISO 8601 date format and of special characters and spaces.