Reading RTD Temperature Sensor
There are a few places to look.

First of all you should have some analogue filtering before you sample. Temperature measurements are usually slow changing so it should be possible to filter fairly aggressively. Even a simple RC can be very effective.

Consider how much cable you have between the circuit and the RTD. Where is that cable running in relation to other (potentially noisy) cables? Separation between wiring looms and reducing the length of the cable can both help in this case. As can better quality shielded and/or twisted pair wiring.

If you have access to an oscilloscope you should try and measure the voltage signal that you see going into the adc. Assuming that there is noise present, the nature of the noise will give some hint as to where it's coming from.

Consider how the sensor and you uC circuit are grounded with regard to what ever it is you're measuring. If the RTD is connected to an earthed object it is possible that the noise is being coupled as a result of an earth loop.

If you can post more details of the circuit you have, how you're filtering the samples and the application, it should be possible to provide some more specific feedback.