Okay, the original Smart Extruder has many issues. I've clocked about 60 hours on a new Replicator+ w/ Smart Extruder+ and haven't encountered any of the issues I heard about with the original extruder. So, I might begin by re-recommending what MakerBot Industries has recommended to their customers which is upgrade your Smart Extruder to the new Smart Extruder+.
However, the extruder may not be completely at fault. A picture says a thousand words, so if you have one, please add one. Based on your description of the part's layers "thinning out", double check your extrusion settings in MakerBot Desktop.
Another potential issue is too much tension on the filament as it is being fed into the extruder. Here are some things that can lead to too much tension:
- Filament wound around spool/spool holder
- Filament kinked
- Too much friction between the spool and spool holder
- Too much friction between the filament and the filament guide (the plastic tube)
Finally, and my reason for bringing up the Smart Extruder, is that your extruder may be clogged or "gumming up". In the past, if there was too much tension on the filament and the drive gear was not adjusted correctly, the drive gear would grind the filament. This would lead to small deposits of filament gumming up the drive gear, eventually leading to the filament slipping. Once the filament began slipping, it would slowly no longer extrude and heat up further up the extruder assembly. This inevitably leads to the extruder becoming clogged. In short:
{Too much filament tension} + {Too tight drive gear} = Gumming
{Too much gumming} + Time = Slipping/"Thinning"
{Too much slipping} + time + heat = Clogging