Partially copy a folder, preserving the invisible system files contained, but only some of the remaining content
First create a new folder where you will copy the data to: mkdir &lt;dest_folder&gt;. Then use:

# "First level" hidden files
find &lt;source_folder&gt; -d 1 -name ".*" -print0 | xargs -0 -J % cp -R % &lt;dest_folder&gt;
# Normal folders
cp -R &lt;source_folder&gt;/&lt;folder1&gt; &lt;source_folder&gt;/&lt;folder2&gt; ... &lt;dest_folder&gt;