$ cat fl
folder1/file1
folder2/file3
folder2/file5
folder3/file2
$ cat script 
cat fl | while read line ; do
  echo "line = $line"
  echo " :: file   : ${line#*/}"
  echo " :: folder : ${line%/*}"
  echo " :: command: mkdir -p ${line%/*} && mv ${line#*/} ${line%/*}"
done 
$ bash script 
line = folder1/file1
 :: file   : file1
 :: folder : folder1
 :: command: mkdir -p folder1 && mv file1 folder1
line = folder2/file3
 :: file   : file3
 :: folder : folder2
 :: command: mkdir -p folder2 && mv file3 folder2
line = folder2/file5
 :: file   : file5
 :: folder : folder2
 :: command: mkdir -p folder2 && mv file5 folder2
line = folder3/file2
 :: file   : file2
 :: folder : folder3
 :: command: mkdir -p folder3 && mv file2 folder3