I have a signal with frequency of 1000 Hz, and it consist of velocities of an hot-wire. The measurements are taken behind a cylinder as air is blown on the cylinder. When i process the signal of each of the cases (different start velocity) I get an extreme value at the start, just a single point. What is the best way to treat this, because it is an abnormality and I should "remove it"?
This is just a quantity proportional to the 0-th frequency of your signal, in other words the average value. It is not abnormal, since it is necessary to have an invertible Fourier transformation.
If you want to remove it, you can just remove a central tendency (like the mean) from your signal (windowed or not).