If you have your data stored inside AnimalTrack objects, then it should be fairly simple to loop through all the TimePoints inside an AnimalTrack object, printing out something like:
chickID1,time1,x1,y1
chickID1,time2,x2,y2
...
chickID2,time1,x1,y1
chickID2,time2,x2,y2
...
You could print it out to the console first, and once that's working, switch it over to print to a PrintWriter attached to a FileWriter. To make a CSV file (comma-separated-value) file that you can open in Excel, you can simply create a text file that has numbers in it separated by commas. (You learned how to print things to text files back in CSC 211... Chapter 6, if you still have your textbook...)