Let us start from the top. Assuming you have LDOPE installed on Windows, you can start working with it.
To open the command line, you open start and search for and run
With the command line open, you can maneuver to the place where you have your data. To maneuver around you need to use the
cd-command. cd is short for 'change directory'. If you need to get to another harddrive on your computer, you must do that specifically. For example, to get to the d-drive, you type d:\
Once you are in the right folder (where your data is located), you can run the commands as described in the manual, for example:
unpack_sds_bits -sds=Cloud_Mask.1 -bit=1-2 -of=cloud_bits.hdf MYD35_L2.A2002189.2040.003.2002191125354.hdf
Which would take the raw MODIS file, go into the Cloud_Mask.1 sds, extract bits 1-2 and write that to cloud_bits.hdf.
Assuming your installation of the software went correctly, the above should work. If you get errors you should check your environmental variables (which is well documented on numerous sites findable using google). You have to make sure that the folder where you installed LDOPE is in the PATH variable.
If you get it to work on one file, the next lesson would be to automate the processing of many files. This is best done using what is commonly referred to as bat-files, which in essence simple run many command line commands in a row, which you can have pre-fabricated using many different approaches.