Keep in mind this is all speculation as I have no proof nor does anyone really. My opinion and theories are based on what I have read and people I have spoken too. I have spoken to several people who claim to be abductee's and they aren't what you'd expect. They are normal people who never even thought about "aliens" until for whatever reason the figured out what was going on. Most have been to hypnosis to find out what is happening to them. The rest seem to just be over paranoid for no reason. Anyway,
firstly the reason I think our scientists are baffled is because we still have yet to figure out how the hell their ships work- it seems to be magnetics or something similiar and even if we could figure it out we couldn't pilot them because our bodies contain too much mass(some more than other eh Frack!). That seems to be why they are short and skinny, less mass equals less stress on their bodies when changing direction so quickly.
I think if even the most secret group had info on what they are up to or what makes them tick it would somehow seep into our technologies or rumors would get out at the least. Granted I'm sure some have but nothing major. As for what I mean by organic- I mean that their propultion systems and flight instruments as it were are most likely not like ours at all. They would more likely be more integrated into the actual crew as opposed to a flight stick of something. Magnetics of some kind seems to be a good guess. Think of it this way, think where we are at with DNA research and gentics in the year 2002. Now, we are damn close to making clones right? Well, now take a small device like an MP3 player, they are pretty small and able to hold 20G's of music right? Several year ago both would be unheard of. Now, imagine a race of people that is literally light years ahead of us in technology- it would be nearly impossible to imagine how they would get around or even go about their day. They probably have tiny microcomputers that can think on their own and are practically living beings themselves. That is how I mean organic. That is where technology seems to be headed. So I make the logical jump ahead and figure they would do the same. I think link between technology and living things will blur even more in the future and with aliens they appear to one and the same.