It sounds like you are interested in cleaning up this mess without creating an even bigger mess. However, if this employee can quickly access what she needs and is able to do a solid job, it may be worthwhile to literally take a step back and focus less on her work area and more on her work.
You obviously have a very competent employee, and it could even be argued that part of her success is due to her rather unique filing system. If you are concerned about what visitors might think, remember that they too are more interested in work than workplaces. Besides, you can always close the door to this office.
Although this employee is not setting a great example for her employees when it comes to filing, the quality of her work is apparently setting a very good example. Besides, there are many extremely neat offices from which nary a shred of work ever emerges.
However, there is an important reason for her to do some housekeeping, especially in terms of papers on the floor, and that reason is safety. People can trip, slip, and fall as a result of the mess. As a result, a little training and perhaps some furniture changes can help turn these piles into files.
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