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Stencil thickness makes a difference! Thicker stencils allow more paste to be deposited which is good for large parts and connectors but can cause shorts with finer pitch parts.
To calculate the optimal stencil thickness for fine pitch placement, IPC standard #7525 states:
Stencil Thickness = 2.64 + 0.0831 * Pitch of component (in mils)
So, say for an FT232RL chip, which is a SSOP part with 0.65mm pitch. First figure out the pitch in thousands of an inch:
0.65 mm / 25.4 = 0.0256 inches = 25.6 mils
Then calculate according to the equation above
2.64 + 0.0831 * 25.6 = 2.13 + 2.64 = 4.77 mil
So for SSOP parts, 4 to 5 mil is the thickest you should go