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Compacting VirtualBox Disk Images - Linux Guests
  1. Start the Linux virtual machine;
  2. Clean the free space on the disk of the Linux virtual machine; 
    dd if=/dev/zero of=zerofillfile bs=1M
    • if= specifies the input file;
    • /dev/zero indicates a bit-stream of zeros
    • of= specifies the output file
    • zerofillfile name of the file containing the bit-stream of zeros
    • bs= indicates the block size
    • 1M indicates that the block size will be 1 megabyte
    rm zerofillfile
  3. Shutdown the Linux virtual machine;
  4. Use the VirtualBox VBoxManage utility to compact the Linux guest image.

Ref: Compacting VirtualBox Disk Images - Linux Guests