Meny click runs above timer or waits?

Hi.
I have a forms.Timer and also a ContextMenuStrip.
When the timer ticks it runs a long sub() .
My question is, if I select something on the ContextMenuStrip, while the sub of the timer is running, will it wait for the sub to finish or interfere?
My 2 cents goes on waiting to finish since this is not a tread.timer but I'm not completely sure, since, for example if I show a messagebox , I can see that the timer is running on the background,
even if the messagebox halts the function until keypress. That is strange because I was under the impression that the messagbox runs on the UI thread and it will block the timer, but?...

If that is also the case when clicking a ToolStripMenuItem while the item is running then , how can I prevent this?

Thanks.