Hi Mark,
Atypical cells on cytology can be very difficult to interpret. Although malignant cells can be atypical (as opposed to "SUSPICIOUS") inflammation and infection can have atypical cells as well. Repeating the cystoscopy, cytology in 3 months is a good idea. I would also suggest a CT scan of the kidneys to complete the work-up. A history of smoking would also make me more suspicious. Atypia does not necessarily mean pre-cursor, it does not correlate well with "pre-malignant" conditions.
Thanks again for your time and for providing a better picture of urine cytology results.