Where does CLion store executable files?

When you build under CLion,

It prints the path it sends the executable to the Console:

-- Build files have been written to: /home/<user>/.clion10/system/cmake/generated/8bd932b1/8bd932b1/Debug1

To change this File > Settings..., and under CMake settings, enter the desired subdirectory name (e.g., ‘bin’) in the Working directory field:

(You may require Run > Clean before the new output path is used.)