For your context, I would suggest one of the variations of indent. You might also be able to change protruding (adj.) to protrusion (n.) and use cavity as the antonym :-)

17. protrusion pro TROO zhun something sticking out
Synonyms >> Antonym >> indentation
A large protrusion on his head was the result of being hit by the bat.
Derivatives >> protusive, protusively, protusiveness
http://fmhs.lisd.net/summer/psatteam/vocab/Voc Lesson 28.pdf

protrusion
–noun
1. the act of protruding or the state of being protruded.
2. something that protrudes or projects.
http://dictionary.reference.com/search?q=protrusion

indent–noun
12. a toothlike notch or deep recess; indentation.
http://dictionary.reference.com/search?q=indent

An information storage medium and a method of recording data on and/or reproducing data from the information storage medium, includes an information storage medium having at least one information storage layer. Data is recorded in the form of protruding or indented pits in the entire or partial area of the information storage medium, and information regarding the protruding or indented pits is recorded. Smooth tracking can be achieved using the information regarding the protruding or indented pits, that is, push-pull polarity information.
http://www.wipo.int/pctdb/en/wo.jsp?wo=2004105000

Only one microstructure is shown on each side of the tool tip for illustrative purposes only; the tool tip can have any number of microstructures and any shape, dimension, and configuration of them. As an alternative to an indenting microstructure, machined tool tips can have protruding microstructures, or a combination of indenting and protruding microstructures.
http://www.wipo.int/pctdb/en/wo.jsp?IA=US2007067201&wo=20071...

Temperature-controlled reversible surface protrusions can be made on NiTi shape memory alloys and thin films as a result of indentation induced two-way shape memory effect. First, spherical indents or scratches are made on the surface of a NiTi alloy in its martensite phase. Second, the indented or scratched surface is planarized to restore a flat surface. Reversible circular and line protrusions are produced by altering the temperature to drive the martensite to austenite phase transformation. This phenomenon can be exploited for a wide range of optical, tribological, and microelectromechanical device applications. ©2006 American Institute of Physics
http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=n...

1. A process to form microstructures comprising: disposing a slurry comprising a mixture of a ceramic powder and a curable fugitive binder on a glass substrate patterned with a plurality of electrodes; shaping the slurry into a plurality of microstructures disposed on the substrate with a patterned mold by contacting the slurry with the patterned surface of the mold to fill indentations of the mold,
http://www.patentgenius.com/patent/7429345.html

[0035] The material for forming the microstructures on the patterned substrate can be placed between the mold and the substrate in a variety of ways. The material can be placed directly in the pattern of the mold followed by placing the mold and material on the substrate, the material can be placed on the substrate followed by pressing the mold against the material on the substrate, or the material can be introduced into a gap between the mold and the substrate as the mold and substrate are brought together by mechanical or other means. The method used for placing the material between the mold and the substrate depends on, among other things, the aspect ratio of the structures to be formed on the substrate, the viscosity of the microstructure-forming material, and the rigidity of the mold. Structures having heights that are large compared to their widths (high aspect ratio structures) require molds having relatively deep indentations. In these cases, depending on the viscosity of the material, it can be difficult to completely fill the indentations of the mold unless the material is injected into the indentations of the mold with some force. In addition, care should be taken to fill the indentations of the mold while minimizing the introduction of bubbles or air pockets in the material.
http://www.freepatentsonline.com/y2001/0007682.html

14. A method of forming a microstructure bearing article that exhibits reduced groove tip impression, the method comprising:
preparing an oligomeric composition;
depositing the oligomeric resin composition onto a master negative microstructured surface or onto a substrate in an amount barely sufficient to fill cavities of the master;
filling the cavities by moving a bead of the oligomeric resin composition between the substrate and the master, at least one of which is flexible, the oligomeric resin composition forming the desired microstructure;
curing the oligomeric resin that forms the desired microstructure; and
heat treating the desired microstructure at a temperature that is at least equal to a normal glass transition temperature of the resin, the heat treating raising the glass transition temperature of the resulting polymer above about 333° K. such that groove tip impression is reduced.
http://www.freepatentsonline.com/5626800.html

The viscosity of the oligomeric composition as deposited in step b) preferably is within the range of about 1,000 to about 5,000 centipoise ("cps"). Above that range, air bubbles might tend to be entrapped, and the resin might not completely fill the cavities of the master molding surface. Below that range, the resin would tend to shrink upon curing to such an extent that the cured resin may not faithfully replicate the master molding surface. Preferably, the viscosity of the resin is between about 2,000 and about 3,000 cps. Within that preferred range, the oligomeric composition should completely fill the master cavities without any need to apply pressure. However, when the cavities are unusually deep and/or narrow, it may be desirable to reduce the viscosity below 2,000 cps, because some shrinkage is to be preferred over any failure to fill the features completely.
http://www.patentgenius.com/patent/5254390.html



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Note added at 1 day5 hrs (2009-02-14 03:46:56 GMT) Post-grading
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Thank you for the kind words, ysun :-) Till next time, happy translating!