Sure, there's lots of functionality that can help you. Here is an example.
First, I made up some "fake" data for myself. I have a 100x100 matrix where, in the 15th column, I set elements 1 through 15 and 75 through 100 to NaN. You can try it with your data if you'd like:
x = rand(100);
x([1:15,75:100], 15) = NaN;
Next you can pick out the "valid" indices of this column by logical indexing using the "isnan" function. Note that you want the values that are NOT NaN, hence the "~".
validIndices = ~isnan(x(:,15))
You can use these to index into the 15th column of your data. Just to verify, you can display the size of the vector.
myVec = x(validIndices,15)
Finally, if you want to flip the matrix, you can use the "flipud" (flip up-down) function:
If you're one of those people who prefers borderline illegible one-liners to show off their MATLAB prowess, you could always do this:
myVec = flipud(x(~isnan(x(:,15)),15));