I need some help with the Fourier transformation of my data.
My original data is a Distance VS Time:

upon doing a Fourier Transform, I get the following:

I understand that normally after a Fourier transform the data is translated to amplitude/power VS frequency
But I am failing to understand what it is showing on the two axis? .
Also why some of the values are negative when my original data has all positive values?
Any suggestions?
UPDATE 1
After plotting the absolute values I get the following:

So now I can recognize that the x- axis is time, but I still cannot make out the y - axis, is it frequency?
UPDATE 2
Performed a FFTSHIFT so it looks more like this:

which i think is a proper representation except it is still maintaining the same x -axis.
I would look for an error in how you used the plot command. The second plot looks more like a programming error than anything else.
The output of a Fourier transform is usually a set of complex numbers. It looks like in the second plot the numbers are being plotted on an Argand diagram.
Try plotting the real parts, the imaginary parts, or the absolute values of the outputs of the Fourier transform.