<p>All of a sudden I seem to be having a lot of issues with under extruding on my Ender 3. The bottom layer (of height 0.1&nbsp;mm) prints perfectly fine. This is done at 15&nbsp;mm/s speed. However, The moment the print moves to layer 2 and above (at the default speed of 60&nbsp;mm/s), I start hearing a lot of clicking noise on the extruder.</p>

<p>So far I have tried the following</p>

<ul>
<li>Replace nozzle to eliminate clogs</li>
<li>Cleaned the inside of the hot end assembly</li>
<li>Calibrated extruder steps/mm</li>
<li>Reduced the layer height from 0.3&nbsp;mm to 0.2&nbsp;mm</li>
<li>Reduced feed rate to as low at 50&nbsp;%</li>
<li>Cleaned the filament feeder assembly and verified that it is able to push the filament properly (Extruding when the print is not happening works just fine with no clicking)</li>
</ul>

<p>Even with all the above, the issue is still persisting. I am not what else could be causing this. </p>

<p>I am printing with PLA at 200 C</p>

Not allowed to comment, so have to answer:
The temperature sensor is a thermally sensitive resistor. Unfortunately, the temperature is near the high limit of that sensor, and the manufacturing tolerances are very significant. That is why a temperature tower is important for each printer, as well as each filament. (I have 4 printers and each requires a different temperature for the same filament. My worst-case is out by 25 degrees! - it's the one I bought second-hand because the original purchaser couldn't get it to work. I could replace the NTC, but it is easier just to have settings to suit that printer.)
Filament does change over time. Lots of theories about why, but the practical response is to tune settings to suit the filament. The alternative is to modify the filament (eg drying, adding oil to surface, etc.), but even with really old filament, I've found adjusting settings (in the slicer, like Cura) to be the most generally workable solution.
Bottom line is to test, adjust settings and repeat until the system achieves the result you need. Treat most recommendations as serving suggestions, so use them as clues (but not rules) for the puzzles presented as 3D printing.