I work for Massachusetts company and I am an exempt employee. My employer is going to start to mandate that all exempt employees punch in an out using a time clock. Can you tell me if I work over 40 hours and it is confirmed by the time clock, does my employer have to pay overtime to me for all hours worked over 40.

No. Nothing in Federal law, Massachusetts law or the law of any other state says that if you are required to punch in and out you are automatically non-exempt and entitled to overtime. It is perfectly legal to require an exempt employee to punch in and out, and there can be some perfectly valid reasons for doing so; i.e. keeping track of hours for 401k, FMLA or other benefit purposes, billing clients for the employees' time, or even safety - one company I know began requiring all employees to punch in and out so that they'd know who was in the building in case of fire, etc.

It is only if they amend your pay to reflect the hours worked that the exemption would be jeopardized, and if the exemption is not jeopardized they do not owe you overtime.

I agree with cbg fully.

One other thought: Even though you state that you are an "exempt employee" (hence, cbg's answer to your query), you should double check to make sure that's true. Many employers and lots of people posting questions on this site misclassify employees as exempt.

If indeed that's true (and there's no reason to suspect otherwise from your post), then there's nothing more to add. If not, cbg and I have lots to tell you.