FFT filter to remove cd scratch
This approach with notch filter with not work. All clicks are impulse-like sounds and we know that an impulse has frequency content at almost every frequency. What you are trying to do, by applying the $6 \ \texttt{Hz}$ notch filter is to remove sinusoid with that particular frequency in your signal, isn't it? So do you hear that your clicks are such low-frequency sounds? Definitely not! Those clicks are spreading into whole of your spectrum (like very short burst of noise), and filtering out $6 \ \texttt{Hz}$ won't help!.
You also didn't shared any more informations about nature of your clicks and a signal (spectrogram, waveform or even recording would be great), because it might be the case that your signal is also impulse-like (i.e. recording of a shooting range), which will make the recognition and cleaning task bit more complicated. Also are your clicks the same over time? This could be also the case for digital systems, and simple correlation calculation should do the job. Additionally if you can sacrifice some of your recording quality and click's are very short, then you can use the median filtering. You can also use some time-frequency methods (based on wavelets, spectrogram calculation, LPC's) or  statistical approach, such as AR modelling, etc.
Here is some reading for you - I hope it will guide you and you will find appropriate method for your kind of signals.

Audio Click Removal using LPC
Godsil S., Rayner P. - Digital Audio Restoration - lot's of references
AR modelling based approach - book chapter
Detection of clicks using sinusoidal modelling for the confirmation of the clicks
Automatic detection and removal of impulsive noise in audio signals