We outline a technique to create three-dimensional topographic maps of the Earth's ionosphere. Using all-sky images at 630.0 and 777.4 nm taken with the Cornell All-Sky Imager (CASI) while located at the Arecibo Observatory, we can estimate the maximum density (Nm) and the height (Hm) of the F layer over a 1000¿1000 km area. This is possible because to first order, the 777.4 nm emission, produced by radiative recombination, is proportional to the integral of the square of the plasma density, whereas the 630.0 nm line, produced by charge exchange and dissociative recombination, depends on both plasma height and density. Using the neutral atmosphere given by the Mass Spectrometer Incoherent Scatter (MSIS-86) model and electron densities from the international reference ionosphere 1995 (IRI-95) model, we show that the estimates given by these maps are good to within 5% of the values used as input into the models. These errors are slightly larger (10%) when extreme gradients in the height of the F layer are present. We apply our technique to two different nights in 1999. In one example these maps show a steeply rising ridge of ionization stretching equatorward of the Caribbean site, punctuated by a series of parallel ridges and valleys. We compare these observations with previous work at Arecibo during very high magnetic activity. In our case we find no evidence for particle precipitation and agree with Sahai et al. [1981a> that spatial variations may have affected the earlier study. Another example shows the Appleton anomaly much farther north than normal. Instability processes are indicated in the former case, while physical mechanisms associated with a magnetic storm are explored in the latter case. ¿ 2001 American Geophysical Union