You can use plot3(X1,Y1,Z1,...) to plot 3D nodes. X1 is the third column in swc file, Y1 is the fourth column, and Z1 is the fifth column.

But if you also want to plot 3D tree structure, you may need to find the way on your own. My suggestion is to process the swc file in MATLAB, and display it in Vaa3D.