You can get this information easily in the latest version of MATLAB, which is R2018a. The function you need to use is findNodes.
Here is a simple example with block as geometry:
model = createpde; gm = importGeometry(model,'Block.stl') msh = generateMesh(model); vertexNodes = findNodes(msh,'region','Vertex',1:gm.NumVertices); vertexCoordinates = msh.Nodes(:,vertexNodes)