The present invention relates to a method for producing a substrate with at least one covered via that electrically and preferably also thermally connects a first substrate side with an opposite second substrate side. The processing involves forming a trench on a the first substrate side remains and covering the trench with a permanent layer on top of a temporary, sacrificial cap-layer, which is decomposed in a thermal process step. The method of the invention provides alternative ways to remove decomposition products of the sacrificial cap-layer material without remaining traces or contamination even in the presence of the permanent layer. This is, according to a first aspect of the invention, achieved by providing the substrate trench with an overcoat layer that has holes. The holes in the overcoat layer leave room for the removal of the decomposition products of the cap-layer material. According to the second aspect of the invention, opening the covered trench from the second substrate side and allowing the cap-layer material to be removed through that opening provides a solution. Both methods of the present invention are based on the common idea of using a temporary cap-layer even in a situation where the substrate opening is permanently covered before the removal of the temporary cap-layer.