Begin with planning. Decide what parts of the painting you will and will not recreate. Brainstorm some different ideas for what materials to use for your various items. Twigs make excellent bare trees and cotton balls can make wonderful clouds. Molding and polymer clay will be the best tools to use for any custom shapes you will need. Look online and locally at some model shops for tiny lamp posts, benches and even little houses.
Gather your materials. Do your best not to leave anything out. You will need a ground surface, most likely, as well as people, animals, plants and other textures. For glass try aluminum foil or some page protectors.
Cut and paint your box. If you are using a shoe box, simply remove the top for a bird's-eye view diorama, or cut one side out of any box for a frontal view diorama. Leave the top on if you would like to hang anything like clouds, birds or stars. Paint the box black inside and out to prepare for creating your scene.
Lay all the objects out first. It is very important to arrange items in your diorama before gluing anything down. If you want the ground or sky to be painted, do so now. Once you have arranged everything and it looks just the way you like, you can use your hot glue gun. Don't use too much or your diorama will end up looking messy; one small dot should be sufficient.
Add any small details to the finished project. Paint the outside if you like, or leave it black to draw attention to the inside of the box. Make sure you sign your work somewhere so everyone knows who created this new 3D model.