Silica layers implanted with Si and Er ions to various doses and annealed at 950 degrees C have been investigated by means of energy-filtered transmission electron microscopy (EFTEM) and high annular angle dark field (HAADF). EFTEM analysis reveals Si nanoclusters (Si-nc) with an average size around 3 nm for high Si content (15 at. %) whereas no clusters can be imaged for the lowest Si excess (5 at. %). Raman scattering supports that amorphous Si precipitates are present in all the samples. Moreover, the filtered images show that Er ions appear preferentially located outside the Si-nc. HAADF analysis confirms that the Er atoms form agglomerations of 5-10 nm size when the Er concentration exceeds 1x10(20) cm(-3). This observation correlates well with the reduction of the Er population excitable by Si nanoclusters, in the best case corresponding to 10% of the total. A suitable tuning of the annealing drastically reduces this deleterious effect.