Before, I can answer your question, do you have a Freeze Drying apparatus ( Lyophilizer)
Vernon L Reisenbichler is right. If you don't have one, try to find someone with space you can use on theirs, especially if it up and running frequently.
In addition to the instrument you'll need to be able to connect a compatible vessel (of appropriate volume and material). You can Google "lyophilizer" and then select Images for examples.
The process specifics depend on your enzyme. Try to find a method in the literature that you can replicate. Otherwise consider the robustness of your enzyme. Many can be lyophilized from a solution in dilute PBS. Others require a stabilizer, like trehalose.
You'll want to have an assay for the specific activity of your enzyme, so you can measure loss of activity due to the process steps.
To maintain enzyme activity and prevent protein aggregation, it may be helpful to include an excipient in the enzyme solution for lyophilization, such as sucrose or trehalose.
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