If I get your question correctly, you are attempting to differentiate the various subtypes of RNA using enzymes that are specific to eachl type of RNA (mRNA, tRNA and rRNA). If this is true then below are some suggestions.

To differentiate RNA molecules in this dispensation of next generation sequencing, sequencing is the best method not enzymatic techniques. After sequencing, the bioinformatics tools can easily help you to identify the subtypes of the RNA.

However, if your focus is to know enzymes that are specific to or can modify the subtypes of RNA then you need to screen for different enzymes (that relevant literatures have shown to have activities for your RNA subtypes) and use molecular docking software to see if the rRNA, tRNA or mRNA will have binding sites to the enzymes.

tRNA are usually post transcriptionally modified by RNA polymerase, tRNA methyltransferase, etc.

You can browse some other enzymes that use may use

Hello, Dr. Spencer. I am very confused as well with the instruction given to me by my professor. Since he told me to propose a workflow using enzymes in molecular biology to distinguish RNA types from one another. From what I understand based on his instruction, I think he meant to propose an enzyme assay. Although I am not sure about it so I asked for clarification.

Yes, I agree with the information you've said. You've explained it explicitly and I've gained additional knowledge with your explanation, sir. I will get back to you once my concern has been clarified. Thank you very much!