Several companies make modular DC-DC converters for jobs like this. You might be able to puck one up on eBay or similar. They take something like 12 V DC and put out 1000 - 2000 V, unregulated. Then, with some high-value resistors and a FET-input op-amp, you make a voltage measuring circuit. Then, with another op-amp and a Darlington power booster, you make a regulator loop that drives the DC-DC converter. You can put a couple pole R-C filter after the DC-DC converter to remove any noise. It is a little tricky to get the regulator loop to close around the R-C filter, but with some care, you can make it stable. I've built a couple of these, many years ago.
Jon