dds <- DESeq(dds) results <- results(dds) filteredResults <- results[which(abs(results$log2FoldChange) > 1 & results$pvalue < 0.05),] write.csv(as.data.frame(filteredResults), file = "DESeq2_filtered_results.csv")

I am attaching the picture of the filtered results, I am still getting log2fold change values in negative output of the filtered results, how should I resolve this?

You are filtering absolute logFC, and in your code that gives you all logFC below -1 and above 1, I see no issue here. You probably want to filter on padj though, see the vignette.