HARP only allows for a reduction in the rate on the first mortgage. Paying off a second mortgage is considered a cash out transaction, and those are not allowed. Asking FNMA will do no good, it’s been a hard and fast rule since the first day HARP started.
If you’re able to lower the rate/payment on the first, and if the second is presumably at a higher rate, consider using the monthly savings on the first to pay more on the second and get it paid off sooner. At least it would be better than nothing!