Organizing data and files
I have been using a very simple system and am very happy with it:


have one projects directory
have one private directory
have one life directory


Inside these directories, I create one new directory per year, for example projects.2015.
Inside this directory, each new sub project gets its own folder that starts with the date at which I begun this new project, for example 20150902 rendering performance analysis. Everything related to this project will be placed inside this directory, no matter when it is done.

When your projects get too complex, you can always add a text file describing the content of your files in more detail, and place this file inside the projects.2015 folder. However, do not place anything else in this folder! Only folders starting with a date and maybe one file giving more information.

This system has worked for me for about ten years and I see the following advantages:


very easy to implement
does not depend on software that may or may not be available in 5 or 10 years
works on Mac, windows, Linux, etc
can be backed up easily, for example by placing your files on your cloud storage folder
future ready: when I started online backup, for example, did not exist yet and we do not know what will exist in the future; but system will probably be compatible.
very comprehensive: chances are you will remember what year and maybe what month you did a specific project, so it will be very quick to find your stuff.


Finally, if many projects contain a similar structure, stick to an identical organization of your data. Whatever your structure, sticking to a system will make it easier to retrieve your files later. For example, inside your folder 20150817 afm study 1055nm grating and any other measurement folder, you could have the following sub folders


00 notes
01 code
02 raw data
03 processed data
04 plots


Personally, I often use numbers because this orders the list of items in my desired way and because in Unix, Mac, etc, I can just type cd 03[tab] and the system auto completes.

Whatever you end up choosing as a system, my recommendation is that you look for something trivial to implement that does not slow you down. The more trivial the logic, the more likely you will stick to it over the years and benefit from the ordering you have. 

Have fun