Hi Amar,
I've checked if there are any example codes for the RTC with the SPC5643L and there is not, I do apologize for the inconvenience this may cause you.
In regards to your question:
also want to clear Alarm Minute Register
What do you mean clear the Alarm Minute Register?
A) Do you want to disable it, so it no longer produces an alarm at any value?
or
B) Do you want to reset the alarm minute to a different value?
A) If you want to disable it, you can handle this in the same control register as AF. You may clear AF and AIE at the same time. 

The AIE bit controls if an interrupt is generated or not from all alarm flags (you will disable all other alarm flags such a s hours, seconds, day and weekday).
If you want to disable only the minute alarm flag then it is the AE_M bit. This will be two steps since they are in different addresses. First clear AF then set AE_M to disable.


B) If you want to reset the value to something different, you must access the register and write a different value to the minute register. So this will be two steps, first clear the AF then access the minute alarm register to write a new a value.
If you do not need a new value, but you want the alarm to be triggered again, then you only need to clear AF. Then alarm will be triggered when the clock has the same value in its minute register.
Best Regards,
Sabina