If it's a 40amp fuse, then it's not the main fuse. It's simply a supply circuit for something high draw or it may be feeding other smaller fuses. There should be more than one of that size fuse.
You need to test the charging to find out if you still have issues there.

It's a little fuse box connected to the positive battery terminal and on top of it the first is main 40a,then,alt 80a and am2 30a and I took my car back to the shop that put the alternator on and they checked it and told me the battery is bad,I just was wondering did that fusible link kill the alternator and batt or is the link related to something else like my headlights not working

Fusible links or fuses don't kill anything, they protect circuits. You can easily test fuses to see if they are good or not but I have no idea what the fuse you are referring to even feeds. The 80 amp would be the only one associated with the alternator so make sure that one has continuity.

Can those be tested with a testlight?

The 40A fuse is for the headlight relay, dome lights, horn and hazard. It is not related to the charging system.

A faulty alternator can kill a failing battery.

Now I know that is related to my headlight problem and yeah its the battery then,thank you so much,appreciate your help

You're welcome.