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You can choose from three different types of files when starting a new one.
New Model File
A Model offers the most flexibility for your voxel scene. To start a new Model file use File > New Model. If Preferences > Start New Model With Empty Matrix is activated, a matrix will automatically be created for you to start editing. Otherwise, you can add a new matrix with Create > Empty Matrix.
New Matrix File
File > New Matrix creates a Matrix as the root node. The entire model must exist inside this Matrix - it is impossible to leave the matrix editor.
New Compound File
File > New Compound starts your scene as a Compound. Starting with a Compound can be useful if your scene needs to be a predetermined size.