One thing I do when replacing fuel filters on the bikes with removable plates in the bottoms of the fuel tanks (916 series, MV, ST series) is remove the fuel pump from the mount plate and clean under it. On these models the pump's rubber sleeve pushes into the mount tube and is held by a raised ring on the sleeve - you can see the corresponding groove in the photo below. You just pull the pump out (possibly easier said than done), maybe lubing the rubber to make it slide nicely. What you often find under the pump at the bottom of the cavity is shown below - lots of debris and rust. I've seen the cavity full to the bottom of the pump screen with gunk.
749 and 999 have a plastic cover held on the the press nut type of steel clip that you can't reliably reuse, and I haven't spent the time to find the replacements for them yet. Probably the same size as those used to hold the fairing insulations on.
It's always a good idea to have a new O-ring on hand when doing this job, as the one that's been in the tank for some time will usually swell as you remove it. Use lots of grease on the O-ring and tank rolled edge when reassembling, as it's fairly easy to take a piece out of the O-ring which will cause fuel to leak at a significant rate. 916 series, ST series and MV models use the Ducati part 88650011A. 749 and 999 use a smaller ring - 88640331A maybe (from memory).
The Aprilias usually have a black plastic screw on cover over the pump pick up screen, so similarly I always remove and clean the pick up cavity when replacing a fuel filter on them. Like the Ducati models with plastic fuel tanks, there isn't a specified fuel filter replacement interval on the Aprilias. I tend to do them on the 20,000/22,500km service depending on the specified intervals for the particular model. In my experience it's worth doing, as even though you don't get any rust inside the plastic tanks you can still get the gummy build ups.
And on all models always check the breather and cap recess drain tubes or hoses through the tank and hoses external to the tank are clear. If you can't blow throught them, they need to be cleaned. Old cable inners are great for this, as they're flexible, but stiff and strong. Just be careful if you're going through plastic or rubber though.