It's actually easy, the steps are as below,
#1 make sure put filter on "select differences" other option to filter out the files you want to copy out.
#2 in the folder filter, select "compare file and folder structure"
#3 right click the root folder to be copied out and select the 'copy to folder’ menu
#4 in the "Folder structure" section, make sure select "Keep relative folder structure"(by default)
#5 select the destination folder