One of the great things about Eagle is the capability built into the tool. One of the capabilities I utilize here to extract smd pad data to make the stencil. Specifically the layers for smd pad solder masks, the top layer is tCream and bottom bCream. They are setup as my layers 31 and 32. Utilizing the dxf.ulp user language program, we can extract the outline data to a dxf file to define the cutter paths to make the stencil. The specific steps I go through to make a solder stencil once the pcb is done is to:

Extract the pad data for the layer to make a solder stencil

To extract the smd pad data in eagle, select only the layers you want to work with for machining. In this image, the bottom layer, holes and dimension layers are active. The dimension (outline of the pcb) is a good reference point, but there is no need to utilize the geometry when cutting. Using the user language program dxf.ulp, the lines will be exported to the dxf file to work with. The croshatching in the image do not export.

Modify the data utilizing a CAD program that works with dxf files.

If you want to add or alter geometry, open the dxf file with your favorite DAD progam and make the appropriate changes. You might for example want to make the cutouts smaller if you are using a simple dxf file to g code converter. Utilizing a CAM program such as CAMBAM, you can define the cutter diameter larger than the actual cutter to reduce the cutout size. So in effect you are fooling the CAM package to calculate cuttor offsets for the G-code to machine smaller cutouts.

Load modified dxf file into CAMBAM to create g-code.

Utlizing select the cutouts then create an Engrave MOP. Typically I define a depth of cut in the -7 to -9 mil region. Simple then have CAMBAM generate the G-code for you and head to the machine to start the milling.

Machine stencil.

MY Youtube Video on the subject