When we have an infection our immune system produces a large amount of white blood cells (WBCs) in our body to fight against the pathogen or parasite. My question is after the immune response has finished fighting the pathogens, what happens to the excess cells and antibodies that presumably are no longer needed? Will they disintegrate themselves, is there a final step in the immune response to dispose of these cells, or are excess of these cells and proteins present as if they are not in excess (they are filtered no more so than when at normal levels)?
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The process you are asking about is called the termination of the immune response, and for a long time it was not studied very much for some reason, with scientists preferring to analyze initiation instead. However, this has changed in recent years, and while we still don't know a good deal, the picture is much clearer than it had been a decade or three ago.
Here is a special edition of Immunological Reviews focusing on termination of the immune response. While the site says you need to pay to access each article, they're actually available for free in PubMedCentral, so just look it up there for access. For a very brief overview, this section of the Wikipedia article on inflammation lists some of the mechanisms involved.
In regards to your question about immune cells and antibodies, a couple of things happen. First, the vast majority of responding cells are either "turned off" or directed to commit suicide (apoptosis) by a variety of signaling mechanisms, such as anti-inflammatory cytokines like IL-4, IL-10, IL-13, and IL-35, along with other molecules like TGFβ and IL1RA, soluble receptors to pro-inflammatory cytokines like TNFα and IL-6, or through "death receptors" like Fas/CD95 and others. However, some cells are prompted to turn into long-lived memory cells, which are able to be quickly activated upon re-exposure to antigen, in many cases completely clearing it without the need for a full-fledged immune response (such as one generating fever and sickness).
As for antibodies, like most circulating serum proteins, they are metabolized mainly in the liver and can be excreted via the kidneys. Their half-lives vary by isotype, but can be as long as three or more weeks. This is assisted by FcRn, the neonatal Fc receptor, which recycles antibodies back into circulation, protecting them from breakdown:
FcRn: the neonatal Fc receptor comes of age
Derry C. Roopenian & Shreeram Akilesh
Nature Reviews Immunology 7, 715-725 (September 2007)
doi:10.1038/nri2155
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$\begingroup$ Good answer. The only thing I would point out, for others reading that may be less familiar with immunology is that you are basically referring to the adaptive response and aren't touching on innate WBCs. $\endgroup$– AMRCommented Aug 24, 2015 at 20:58
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$\begingroup$ @AMR which cells are you referring to as "innate WBCs"? Macs? DCs? Both are involved in antigen presentation and regulation of the "adaptive" response, especially in producing some of the cytokines I mentioned. As time goes on, the line between "innate" and "adaptive" immunity gets fuzzier and fuzzier, and some investigators I know don't even refer to them as such any more, there's so much overlap. $\endgroup$– MattDMoCommented Aug 24, 2015 at 21:50
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$\begingroup$ Neutrophils, eosinophils, basophils, and to a lesser degree natural killer cells. $\endgroup$– AMRCommented Aug 24, 2015 at 21:54
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$\begingroup$ There is however an article on granulocytes that you linked to. When I read your response the first time, the third paragraph sounded like it was focused on the end stages of the adaptive response, but apoptosis is kind of a catch all for the termination of most all the cells raised in an immune response. $\endgroup$– AMRCommented Aug 24, 2015 at 22:09