Begin by preheating the oven to 375°F (190°C). Prepare all ingredients at room temperature, especially the egg yolks, as cold ingredients can affect the texture.
Start with the caramel. Place 3 tablespoons of white sugar (asukal) in each llanera. Heat each llanera over low flame (mahinang apoy), tilting continuously until the sugar melts and turns golden amber. Never stir the caramel while cooking. Once done, set aside to let the caramel harden.
For the custard (pudding), carefully separate the egg yolks from whites while eggs are cold (this makes separation easier). Let yolks reach room temperature. Combine the egg yolks with sweetened condensed milk (kondensadang gatas), gently stirring until well blended. Gradually add the evaporated milk (ebaporadang gatas), vanilla extract, and calamansi zest if using.
Strain the mixture through a cheesecloth or fine-mesh strainer twice to ensure the smoothest possible texture. Let the mixture rest for a few minutes to allow any air bubbles to rise to the surface.
Pour the strained mixture into the prepared llaneras with hardened caramel. Cover each llanera tightly with aluminum foil. Place them in a larger baking pan and create a water bath by carefully pouring hot water halfway up the sides of the llaneras.
Bake for 50-60 minutes. Test doneness by inserting a knife - it should come out clean. Remove from the water bath using tongs and let cool completely at room temperature. Refrigerate for at least 4 hours or overnight until thoroughly chilled.
To serve, run a knife around the edges of the flan and invert onto a serving plate. The caramel will flow over the custard as a sauce. Serve chilled.