It is my understanding Medicare pays Level II codes but because of what is called "carrier discretion", not all insurers pay HCPCS codes. I always code to the highest specificity as the documentation supports. The Q codes in HCPCS are in the temporary code section.
In CPT Cytopathology chapter, the instructions state to use the screening code which best describes the screening method and use an additional code for the preparation, screening, and interpretation. Examples: 88141 and 88164. I don't have the CPT Assistant to refer to but the CPT book refers to several editions which may help you answer your questions. Good Luck.
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