How is the data going to be put on the SD Card?
I assumed from your original post that the Arduino was going to write the data. If so it is easy to make fixed length records even if they are not received as fixed length records.
Can you give an example of 3 or 4 records showing the range of sizes that you need to deal with.
I think it is unlikely there is a structured file system that works within the very limited memory available on an Arduino Uno. Perhaps you need something like a Yun which could have the file system on the Linino side and the hardware interface on the Arduino side.
...R